From 135a5aae229e7ec63c13d8f6f4df7275a039c76f Mon Sep 17 00:00:00 2001 From: ammarcsj <70114795+ammarcsj@users.noreply.github.com> Date: Tue, 16 Jan 2024 18:32:21 +0100 Subject: [PATCH 1/8] make iondf writeout optional --- directlfq/config.py | 10 +++++++++- directlfq/lfq_manager.py | 7 +++++-- 2 files changed, 14 insertions(+), 3 deletions(-) diff --git a/directlfq/config.py b/directlfq/config.py index 5e8a70e..e5037d2 100644 --- a/directlfq/config.py +++ b/directlfq/config.py @@ -5,7 +5,7 @@ def setup_logging(): logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(name)s - %(levelname)s - %(message)s') - +########################## LOG_PROCESSED_PROTEINS = True def set_log_processed_proteins(log_processed_proteins = True): @@ -13,6 +13,7 @@ def set_log_processed_proteins(log_processed_proteins = True): LOG_PROCESSED_PROTEINS = log_processed_proteins +########################## PROTEIN_ID = 'protein' QUANT_ID = 'ion' @@ -22,3 +23,10 @@ def set_global_protein_and_ion_id(protein_id = 'protein', quant_id = 'ion'): PROTEIN_ID = protein_id QUANT_ID = quant_id +########################## +COMPILE_NORMALIZED_ION_TABLE = True + +def set_compile_normalized_ion_table(compile_normalized_ion_table = True): + global COMPILE_NORMALIZED_ION_TABLE + COMPILE_NORMALIZED_ION_TABLE = compile_normalized_ion_table + diff --git a/directlfq/lfq_manager.py b/directlfq/lfq_manager.py index f79e862..d100e82 100644 --- a/directlfq/lfq_manager.py +++ b/directlfq/lfq_manager.py @@ -22,7 +22,7 @@ def run_lfq(input_file, columns_to_add = [], selected_proteins_file :str = None, mq_protein_groups_txt = None, min_nonan = 1, input_type_to_use = None, maximum_number_of_quadratic_ions_to_use_per_protein = 10, number_of_quadratic_samples = 50, num_cores = None, filename_suffix = "", deactivate_normalization = False, filter_dict = None, log_processed_proteins = True, protein_id = 'protein', quant_id = 'ion' -): +,compile_normalized_ion_table = True): """Run the directLFQ pipeline on a given input file. The input file is expected to contain ion intensities. The output is a table containing protein intensities. Args: @@ -38,6 +38,7 @@ def run_lfq(input_file, columns_to_add = [], selected_proteins_file :str = None """ config.set_global_protein_and_ion_id(protein_id=protein_id, quant_id=quant_id) config.set_log_processed_proteins(log_processed_proteins=log_processed_proteins) + config.set_compile_normalized_ion_table(compile_normalized_ion_table= compile_normalized_ion_table) LOGGER.info("Starting directLFQ analysis.") input_file = prepare_input_filename(input_file) @@ -62,7 +63,9 @@ def run_lfq(input_file, columns_to_add = [], selected_proteins_file :str = None outfile_basename = get_outfile_basename(input_file, input_type_to_use, selected_proteins_file, deactivate_normalization,filename_suffix) save_run_config(outfile_basename, locals()) save_protein_df(protein_df,outfile_basename) - save_ion_df(ion_df,outfile_basename) + + if config.COMPILE_NORMALIZED_ION_TABLE: + save_ion_df(ion_df,outfile_basename) LOGGER.info("Analysis finished!") From 360107edf62ce9eda6fa7b91d4eb28e16d625bbc Mon Sep 17 00:00:00 2001 From: ammarcsj <70114795+ammarcsj@users.noreply.github.com> Date: Tue, 16 Jan 2024 18:37:49 +0100 Subject: [PATCH 2/8] speed up table splitting and merging --- directlfq/protein_intensity_estimation.py | 169 ++++++++++++++-------- 1 file changed, 108 insertions(+), 61 deletions(-) diff --git a/directlfq/protein_intensity_estimation.py b/directlfq/protein_intensity_estimation.py index f2c36cb..cac8930 100644 --- a/directlfq/protein_intensity_estimation.py +++ b/directlfq/protein_intensity_estimation.py @@ -29,30 +29,71 @@ def estimate_protein_intensities(normed_df, min_nonan, num_samples_quadratic, nu "derives protein pseudointensities from between-sample normalized data" allprots = list(normed_df.index.get_level_values(0).unique()) - LOGGER.info(f"{len(allprots)} prots total") + LOGGER.info(f"{len(allprots)} lfq-groups total") list_of_tuple_w_protein_profiles_and_shifted_peptides = get_list_of_tuple_w_protein_profiles_and_shifted_peptides(allprots, normed_df, num_samples_quadratic, min_nonan, num_cores) protein_df = get_protein_dataframe_from_list_of_protein_profiles(allprots=allprots, list_of_tuple_w_protein_profiles_and_shifted_peptides=list_of_tuple_w_protein_profiles_and_shifted_peptides, normed_df= normed_df) - ion_df = get_ion_intensity_dataframe_from_list_of_shifted_peptides(list_of_tuple_w_protein_profiles_and_shifted_peptides, allprots) + if config.COMPILE_NORMALIZED_ION_TABLE: + ion_df = get_ion_intensity_dataframe_from_list_of_shifted_peptides(list_of_tuple_w_protein_profiles_and_shifted_peptides, allprots) + else: + ion_df = None return protein_df, ion_df def get_list_of_tuple_w_protein_profiles_and_shifted_peptides(allprots, normed_df, num_samples_quadratic, min_nonan, num_cores): + input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan = get_input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan(normed_df, allprots, num_samples_quadratic, min_nonan) + if num_cores is not None and num_cores <=1: - list_of_tuple_w_protein_profiles_and_shifted_peptides = get_list_with_sequential_processing(allprots, normed_df, num_samples_quadratic, min_nonan) + list_of_tuple_w_protein_profiles_and_shifted_peptides = get_list_with_sequential_processing(input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan) else: - list_of_tuple_w_protein_profiles_and_shifted_peptides = get_list_with_multiprocessing(allprots, normed_df, num_samples_quadratic, min_nonan, num_cores) + list_of_tuple_w_protein_profiles_and_shifted_peptides = get_list_with_multiprocessing(input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan, num_cores) return list_of_tuple_w_protein_profiles_and_shifted_peptides -def get_list_with_sequential_processing(allprots, normed_df, num_samples_quadratic, min_nonan): - input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan = get_input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan(normed_df, allprots, num_samples_quadratic, min_nonan) + +def get_input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan(normed_df, allprots, num_samples_quadratic, min_nonan): + list_of_normed_dfs = get_normed_dfs(normed_df) + return zip(range(len(list_of_normed_dfs)),list_of_normed_dfs, itertools.repeat(num_samples_quadratic), itertools.repeat(min_nonan)) + + +def get_normed_dfs(normed_df): + protein_names = normed_df.index.get_level_values(0).to_numpy() + ion_names = normed_df.index.get_level_values(1).to_numpy() + normed_array = normed_df.to_numpy() + indices_of_proteinname_switch = find_nameswitch_indices(protein_names) + results_list = [get_subdf(normed_array, indices_of_proteinname_switch, idx, protein_names, ion_names) for idx in range(len(indices_of_proteinname_switch)-1)] + + return results_list + + +def find_nameswitch_indices(arr): + change_indices = np.where(arr[:-1] != arr[1:])[0] + 1 + + # Add the index 0 for the start of the first element + start_indices = np.insert(change_indices, 0, 0) + + #Append the index of the last element + start_indices = np.append(start_indices, len(arr)) + + return start_indices + + +def get_subdf(normed_array, indices_of_proteinname_switch, idx, protein_names, ion_names): + start_switch = indices_of_proteinname_switch[idx] + end_switch = indices_of_proteinname_switch[idx+1] + sub_array = normed_array[start_switch:end_switch] + index_sub_array = pd.MultiIndex.from_arrays([protein_names[start_switch:end_switch], ion_names[start_switch:end_switch]], names=[config.PROTEIN_ID, config.QUANT_ID]) + return pd.DataFrame(sub_array, index = index_sub_array) + + + + +def get_list_with_sequential_processing(input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan): list_of_tuple_w_protein_profiles_and_shifted_peptides = list(map(lambda x : calculate_peptide_and_protein_intensities(*x), input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan)) return list_of_tuple_w_protein_profiles_and_shifted_peptides -def get_list_with_multiprocessing(allprots, normed_df, num_samples_quadratic, min_nonan, num_cores): +def get_list_with_multiprocessing(input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan, num_cores): pool = get_configured_multiprocessing_pool(num_cores) - input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan = get_input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan(normed_df, allprots, num_samples_quadratic, min_nonan) list_of_tuple_w_protein_profiles_and_shifted_peptides = pool.starmap(calculate_peptide_and_protein_intensities, input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan) pool.close() return list_of_tuple_w_protein_profiles_and_shifted_peptides @@ -66,65 +107,17 @@ def get_configured_multiprocessing_pool(num_cores): LOGGER.info(f"using {pool._processes} processes") return pool +def calculate_peptide_and_protein_intensities_from_list_of_peptide_intensity_dfs(idx, list_of_peptide_intensity_dfs, num_samples_quadratic, min_nonan): + for peptide_intensity_df in list_of_peptide_intensity_dfs: + calculate_peptide_and_protein_intensities -def get_input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan(normed_df, allprots, num_samples_quadratic, min_nonan): - list_of_normed_dfs = get_normed_dfs(normed_df, allprots) - return zip(range(len(list_of_normed_dfs)),list_of_normed_dfs, itertools.repeat(num_samples_quadratic), itertools.repeat(min_nonan)) - - - - -def get_normed_dfs(normed_df, allprots): - list_of_normed_dfs = [] - for protein in allprots: - peptide_intensity_df = pd.DataFrame(normed_df.loc[protein])#DataFrame definition to avoid pandas Series objects - list_of_normed_dfs.append(peptide_intensity_df) - - return list_of_normed_dfs - -def get_ion_intensity_dataframe_from_list_of_shifted_peptides(list_of_tuple_w_protein_profiles_and_shifted_peptides, allprots): - ion_ints = [x[1] for x in list_of_tuple_w_protein_profiles_and_shifted_peptides] - ion_ints = add_protein_names_to_ion_ints(ion_ints, allprots) - ion_df = 2**pd.concat(ion_ints) - ion_df = ion_df.replace(np.nan, 0) - return ion_df - -def add_protein_names_to_ion_ints(ion_ints, allprots): - ion_ints = [add_protein_name_to_ion_df(ion_ints[idx], allprots[idx]) for idx in range(len(ion_ints))] - return ion_ints - -def add_protein_name_to_ion_df(ion_df, protein): - ion_df[config.PROTEIN_ID] = protein - ion_df = ion_df.reset_index().set_index([config.PROTEIN_ID, config.QUANT_ID]) - return ion_df - - -def get_protein_dataframe_from_list_of_protein_profiles(allprots, list_of_tuple_w_protein_profiles_and_shifted_peptides, normed_df): - index_list = [] - profile_list = [] - - list_of_protein_profiles = [x[0] for x in list_of_tuple_w_protein_profiles_and_shifted_peptides] - - for idx in range(len(allprots)): - if list_of_protein_profiles[idx] is None: - continue - index_list.append(allprots[idx]) - profile_list.append(list_of_protein_profiles[idx]) - - index_for_protein_df = pd.Index(data=index_list, name=config.PROTEIN_ID) - protein_df = 2**pd.DataFrame(profile_list, index = index_for_protein_df, columns = normed_df.columns) - protein_df = protein_df.replace(np.nan, 0) - protein_df = protein_df.reset_index() - return protein_df - - -def calculate_peptide_and_protein_intensities(idx,peptide_intensity_df , num_samples_quadratic, min_nonan): +def calculate_peptide_and_protein_intensities(idx, peptide_intensity_df, num_samples_quadratic, min_nonan): if len(peptide_intensity_df.index) > 1: peptide_intensity_df = ProtvalCutter(peptide_intensity_df, maximum_df_length=100).get_dataframe() if(idx%100 ==0) and config.LOG_PROCESSED_PROTEINS: - LOGGER.info(f"prot {idx}") + LOGGER.info(f"lfq-object {idx}") summed_pepint = np.nansum(2**peptide_intensity_df) if(peptide_intensity_df.shape[1]<2): @@ -200,3 +193,57 @@ def get_dataframe(self): def _get_shortened_dataframe(self): shortened_index = self._sorted_idx[:self._maximum_df_length] return self._protvals_df.loc[shortened_index] + + + + +def get_ion_intensity_dataframe_from_list_of_shifted_peptides(list_of_tuple_w_protein_profiles_and_shifted_peptides, allprots): + ion_names = [] + ion_vals = [] + protein_names = [] + column_names = list_of_tuple_w_protein_profiles_and_shifted_peptides[0][1].columns.tolist() + for idx in range(len(list_of_tuple_w_protein_profiles_and_shifted_peptides)): + protein_name = allprots[idx] + ion_df = list_of_tuple_w_protein_profiles_and_shifted_peptides[idx][1] + ion_names += ion_df.index.values.tolist() + ion_vals.append(ion_df.to_numpy()) + protein_names.extend([protein_name]*len(ion_df.index)) + merged_ions = 2**np.concatenate(ion_vals) + merged_ions = np.nan_to_num(merged_ions) + ion_df = pd.DataFrame(merged_ions) + ion_df.columns = column_names + ion_df["ion"] = ion_names + ion_df["protein"] = protein_names + ion_df = ion_df.set_index(["protein", "ion"]) + return ion_df + + + +def add_protein_names_to_ion_ints(ion_ints, allprots): + ion_ints = [add_protein_name_to_ion_df(ion_ints[idx], allprots[idx]) for idx in range(len(ion_ints))] + return ion_ints + +def add_protein_name_to_ion_df(ion_df, protein): + ion_df[config.PROTEIN_ID] = protein + ion_df = ion_df.reset_index().set_index([config.PROTEIN_ID, config.QUANT_ID]) + return ion_df + + +def get_protein_dataframe_from_list_of_protein_profiles(allprots, list_of_tuple_w_protein_profiles_and_shifted_peptides, normed_df): + index_list = [] + profile_list = [] + + list_of_protein_profiles = [x[0] for x in list_of_tuple_w_protein_profiles_and_shifted_peptides] + + for idx in range(len(allprots)): + if list_of_protein_profiles[idx] is None: + continue + index_list.append(allprots[idx]) + profile_list.append(list_of_protein_profiles[idx]) + + index_for_protein_df = pd.Index(data=index_list, name=config.PROTEIN_ID) + protein_df = 2**pd.DataFrame(profile_list, index = index_for_protein_df, columns = normed_df.columns) + protein_df = protein_df.replace(np.nan, 0) + protein_df = protein_df.reset_index() + return protein_df + From 9788e8bd29e0177ab25063919841b3120ed1a460 Mon Sep 17 00:00:00 2001 From: ammarcsj <70114795+ammarcsj@users.noreply.github.com> Date: Tue, 16 Jan 2024 18:46:40 +0100 Subject: [PATCH 3/8] add test --- .../03_protein_intensity_estimation.ipynb | 726 +++++++++--------- 1 file changed, 383 insertions(+), 343 deletions(-) diff --git a/nbdev_nbs/03_protein_intensity_estimation.ipynb b/nbdev_nbs/03_protein_intensity_estimation.ipynb index 8e2e4d9..c0e6c97 100644 --- a/nbdev_nbs/03_protein_intensity_estimation.ipynb +++ b/nbdev_nbs/03_protein_intensity_estimation.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -11,7 +11,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -47,7 +47,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, "outputs": [ { @@ -97,7 +97,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, "outputs": [ { @@ -172,12 +172,12 @@ " \n", " protA\n", " 0\n", - " NaN\n", + " 44.602965\n", " 44.474241\n", " 41.489085\n", " 43.216307\n", " 43.505708\n", - " 42.338404\n", + " NaN\n", " 43.454211\n", " 43.102621\n", " 41.897534\n", @@ -185,19 +185,20 @@ " 43.261340\n", " 40.203349\n", " 44.447364\n", - " 44.554027\n", + " NaN\n", " 44.692343\n", - " 44.701690\n", + " 44.70169\n", " 43.106703\n", " 44.630975\n", " 43.380650\n", - " NaN\n", + " 43.407413\n", " \n", " \n", " 1\n", " NaN\n", " NaN\n", " NaN\n", + " 33.250522\n", " NaN\n", " NaN\n", " NaN\n", @@ -207,23 +208,22 @@ " NaN\n", " NaN\n", " NaN\n", - " 34.481579\n", " NaN\n", + " 34.726559\n", " NaN\n", " NaN\n", " NaN\n", - " 34.665191\n", " NaN\n", " NaN\n", " \n", " \n", " 2\n", - " 29.73029\n", + " 29.730290\n", " 29.601566\n", " 26.616410\n", " 28.343632\n", " 28.633033\n", - " NaN\n", + " 27.465729\n", " 28.581537\n", " 28.229946\n", " 27.024859\n", @@ -233,7 +233,7 @@ " 29.574689\n", " NaN\n", " 29.819668\n", - " 29.829015\n", + " NaN\n", " 28.234029\n", " 29.758301\n", " 28.507975\n", @@ -245,11 +245,11 @@ " NaN\n", " NaN\n", " NaN\n", - " 38.598817\n", " NaN\n", " NaN\n", " NaN\n", " NaN\n", + " 36.990643\n", " NaN\n", " NaN\n", " NaN\n", @@ -267,30 +267,30 @@ "" ], "text/plain": [ - " 0 1 2 3 4 5 \\\n", - "protein ion \n", - "protA 0 NaN 44.474241 41.489085 43.216307 43.505708 42.338404 \n", - " 1 NaN NaN NaN NaN NaN NaN \n", - " 2 29.73029 29.601566 26.616410 28.343632 28.633033 NaN \n", - " 3 NaN NaN NaN NaN 38.598817 NaN \n", + " 0 1 2 3 4 5 \\\n", + "protein ion \n", + "protA 0 44.602965 44.474241 41.489085 43.216307 43.505708 NaN \n", + " 1 NaN NaN NaN 33.250522 NaN NaN \n", + " 2 29.730290 29.601566 26.616410 28.343632 28.633033 27.465729 \n", + " 3 NaN NaN NaN NaN NaN NaN \n", "\n", " 6 7 8 9 10 11 \\\n", "protein ion \n", "protA 0 43.454211 43.102621 41.897534 43.625508 43.261340 40.203349 \n", " 1 NaN NaN NaN NaN NaN NaN \n", " 2 28.581537 28.229946 27.024859 28.752833 28.388665 25.330674 \n", - " 3 NaN NaN NaN NaN NaN NaN \n", + " 3 NaN NaN 36.990643 NaN NaN NaN \n", "\n", - " 12 13 14 15 16 17 \\\n", - "protein ion \n", - "protA 0 44.447364 44.554027 44.692343 44.701690 43.106703 44.630975 \n", - " 1 34.481579 NaN NaN NaN NaN 34.665191 \n", - " 2 29.574689 NaN 29.819668 29.829015 28.234029 29.758301 \n", - " 3 39.540473 NaN NaN NaN NaN NaN \n", + " 12 13 14 15 16 17 \\\n", + "protein ion \n", + "protA 0 44.447364 NaN 44.692343 44.70169 43.106703 44.630975 \n", + " 1 NaN NaN 34.726559 NaN NaN NaN \n", + " 2 29.574689 NaN 29.819668 NaN 28.234029 29.758301 \n", + " 3 39.540473 NaN NaN NaN NaN NaN \n", "\n", " 18 19 \n", "protein ion \n", - "protA 0 43.380650 NaN \n", + "protA 0 43.380650 43.407413 \n", " 1 NaN NaN \n", " 2 28.507975 28.534739 \n", " 3 NaN NaN " @@ -371,12 +371,12 @@ " \n", " protA\n", " 0\n", - " NaN\n", + " 44.602965\n", " 44.474241\n", " 41.489085\n", " 43.216307\n", " 43.505708\n", - " 42.338404\n", + " NaN\n", " 43.454211\n", " 43.102621\n", " 41.897534\n", @@ -384,19 +384,20 @@ " 43.26134\n", " 40.203349\n", " 44.447364\n", - " 44.554027\n", + " NaN\n", " 44.692343\n", " 44.70169\n", " 43.106703\n", " 44.630975\n", " 43.38065\n", - " NaN\n", + " 43.407413\n", " \n", " \n", " 1\n", " NaN\n", " NaN\n", " NaN\n", + " 43.216307\n", " NaN\n", " NaN\n", " NaN\n", @@ -406,12 +407,11 @@ " NaN\n", " NaN\n", " NaN\n", - " 44.447364\n", " NaN\n", + " 44.692343\n", " NaN\n", " NaN\n", " NaN\n", - " 44.630975\n", " NaN\n", " NaN\n", " \n", @@ -422,7 +422,7 @@ " 41.489085\n", " 43.216307\n", " 43.505708\n", - " NaN\n", + " 42.338404\n", " 43.454211\n", " 43.102621\n", " 41.897534\n", @@ -432,7 +432,7 @@ " 44.447364\n", " NaN\n", " 44.692343\n", - " 44.70169\n", + " NaN\n", " 43.106703\n", " 44.630975\n", " 43.38065\n", @@ -444,11 +444,11 @@ " NaN\n", " NaN\n", " NaN\n", - " 43.505708\n", " NaN\n", " NaN\n", " NaN\n", " NaN\n", + " 41.897534\n", " NaN\n", " NaN\n", " NaN\n", @@ -468,28 +468,28 @@ "text/plain": [ " 0 1 2 3 4 5 \\\n", "protein ion \n", - "protA 0 NaN 44.474241 41.489085 43.216307 43.505708 42.338404 \n", - " 1 NaN NaN NaN NaN NaN NaN \n", - " 2 44.602965 44.474241 41.489085 43.216307 43.505708 NaN \n", - " 3 NaN NaN NaN NaN 43.505708 NaN \n", + "protA 0 44.602965 44.474241 41.489085 43.216307 43.505708 NaN \n", + " 1 NaN NaN NaN 43.216307 NaN NaN \n", + " 2 44.602965 44.474241 41.489085 43.216307 43.505708 42.338404 \n", + " 3 NaN NaN NaN NaN NaN NaN \n", "\n", " 6 7 8 9 10 11 \\\n", "protein ion \n", "protA 0 43.454211 43.102621 41.897534 43.625508 43.26134 40.203349 \n", " 1 NaN NaN NaN NaN NaN NaN \n", " 2 43.454211 43.102621 41.897534 43.625508 43.26134 40.203349 \n", - " 3 NaN NaN NaN NaN NaN NaN \n", + " 3 NaN NaN 41.897534 NaN NaN NaN \n", "\n", - " 12 13 14 15 16 17 \\\n", - "protein ion \n", - "protA 0 44.447364 44.554027 44.692343 44.70169 43.106703 44.630975 \n", - " 1 44.447364 NaN NaN NaN NaN 44.630975 \n", - " 2 44.447364 NaN 44.692343 44.70169 43.106703 44.630975 \n", - " 3 44.447364 NaN NaN NaN NaN NaN \n", + " 12 13 14 15 16 17 \\\n", + "protein ion \n", + "protA 0 44.447364 NaN 44.692343 44.70169 43.106703 44.630975 \n", + " 1 NaN NaN 44.692343 NaN NaN NaN \n", + " 2 44.447364 NaN 44.692343 NaN 43.106703 44.630975 \n", + " 3 44.447364 NaN NaN NaN NaN NaN \n", "\n", " 18 19 \n", "protein ion \n", - "protA 0 43.38065 NaN \n", + "protA 0 43.38065 43.407413 \n", " 1 NaN NaN \n", " 2 43.38065 43.407413 \n", " 3 NaN NaN " @@ -580,94 +580,94 @@ " protA\n", " 0\n", " 44.602965\n", - " 44.474240\n", - " 41.489085\n", - " 43.216306\n", + " 44.474241\n", + " 41.489086\n", + " 43.216307\n", " 43.505708\n", - " 42.338405\n", + " 42.338404\n", " 43.454211\n", - " 43.102621\n", - " 41.897533\n", - " 43.625508\n", + " 43.102622\n", + " 41.897535\n", + " 43.625507\n", " 43.261340\n", - " 40.203346\n", + " 40.203349\n", " 44.447364\n", " 44.554027\n", " 44.692343\n", " 44.701690\n", " 43.106703\n", - " 44.630976\n", + " 44.630975\n", " 43.380650\n", - " 43.407413\n", + " 43.407414\n", " \n", " \n", " 1\n", - " 34.637191\n", - " 34.508449\n", - " 31.523327\n", - " 33.250533\n", - " 33.539906\n", - " 32.372622\n", - " 33.488420\n", - " 33.136837\n", - " 31.931740\n", - " 33.659734\n", - " 33.295572\n", - " 30.237537\n", - " 34.481578\n", - " 34.588245\n", - " 34.726571\n", - " 34.735917\n", - " 33.140931\n", - " 34.665203\n", - " 33.414868\n", - " 33.441634\n", + " 34.637186\n", + " 34.508463\n", + " 31.523287\n", + " 33.250529\n", + " 33.539917\n", + " 32.372627\n", + " 33.488411\n", + " 33.136834\n", + " 31.931726\n", + " 33.659719\n", + " 33.295545\n", + " 30.237605\n", + " 34.481560\n", + " 34.588249\n", + " 34.726569\n", + " 34.735903\n", + " 33.140917\n", + " 34.665190\n", + " 33.414869\n", + " 33.441625\n", " \n", " \n", " 2\n", - " 29.730299\n", - " 29.601596\n", - " 26.616364\n", - " 28.343634\n", - " 28.633164\n", - " 27.465805\n", - " 28.581529\n", - " 28.229941\n", - " 27.024871\n", - " 28.752936\n", - " 28.388685\n", - " 25.330857\n", - " 29.574649\n", - " 29.681455\n", - " 29.819767\n", - " 29.828994\n", - " 28.234112\n", - " 29.758290\n", - " 28.508008\n", - " 28.534752\n", + " 29.730236\n", + " 29.601570\n", + " 26.616213\n", + " 28.343694\n", + " 28.633051\n", + " 27.465858\n", + " 28.581627\n", + " 28.230007\n", + " 27.024935\n", + " 28.752806\n", + " 28.388671\n", + " 25.330804\n", + " 29.574561\n", + " 29.681299\n", + " 29.819709\n", + " 29.828989\n", + " 28.233933\n", + " 29.758262\n", + " 28.507947\n", + " 28.534864\n", " \n", " \n", " 3\n", - " 39.696074\n", + " 39.696073\n", " 39.567350\n", - " 36.582194\n", - " 38.309420\n", - " 38.598821\n", - " 37.431511\n", + " 36.582195\n", + " 38.309417\n", + " 38.598820\n", + " 37.431515\n", " 38.547322\n", " 38.195732\n", - " 36.990644\n", - " 38.718614\n", - " 38.354449\n", - " 35.296454\n", + " 36.990636\n", + " 38.718618\n", + " 38.354450\n", + " 35.296462\n", " 39.540472\n", - " 39.647136\n", - " 39.785450\n", - " 39.794799\n", - " 38.199810\n", - " 39.724082\n", - " 38.473762\n", - " 38.500524\n", + " 39.647137\n", + " 39.785451\n", + " 39.794800\n", + " 38.199811\n", + " 39.724085\n", + " 38.473758\n", + " 38.500527\n", " \n", " \n", "\n", @@ -676,31 +676,31 @@ "text/plain": [ " 0 1 2 3 4 5 \\\n", "protein ion \n", - "protA 0 44.602965 44.474240 41.489085 43.216306 43.505708 42.338405 \n", - " 1 34.637191 34.508449 31.523327 33.250533 33.539906 32.372622 \n", - " 2 29.730299 29.601596 26.616364 28.343634 28.633164 27.465805 \n", - " 3 39.696074 39.567350 36.582194 38.309420 38.598821 37.431511 \n", + "protA 0 44.602965 44.474241 41.489086 43.216307 43.505708 42.338404 \n", + " 1 34.637186 34.508463 31.523287 33.250529 33.539917 32.372627 \n", + " 2 29.730236 29.601570 26.616213 28.343694 28.633051 27.465858 \n", + " 3 39.696073 39.567350 36.582195 38.309417 38.598820 37.431515 \n", "\n", " 6 7 8 9 10 11 \\\n", "protein ion \n", - "protA 0 43.454211 43.102621 41.897533 43.625508 43.261340 40.203346 \n", - " 1 33.488420 33.136837 31.931740 33.659734 33.295572 30.237537 \n", - " 2 28.581529 28.229941 27.024871 28.752936 28.388685 25.330857 \n", - " 3 38.547322 38.195732 36.990644 38.718614 38.354449 35.296454 \n", + "protA 0 43.454211 43.102622 41.897535 43.625507 43.261340 40.203349 \n", + " 1 33.488411 33.136834 31.931726 33.659719 33.295545 30.237605 \n", + " 2 28.581627 28.230007 27.024935 28.752806 28.388671 25.330804 \n", + " 3 38.547322 38.195732 36.990636 38.718618 38.354450 35.296462 \n", "\n", " 12 13 14 15 16 17 \\\n", "protein ion \n", - "protA 0 44.447364 44.554027 44.692343 44.701690 43.106703 44.630976 \n", - " 1 34.481578 34.588245 34.726571 34.735917 33.140931 34.665203 \n", - " 2 29.574649 29.681455 29.819767 29.828994 28.234112 29.758290 \n", - " 3 39.540472 39.647136 39.785450 39.794799 38.199810 39.724082 \n", + "protA 0 44.447364 44.554027 44.692343 44.701690 43.106703 44.630975 \n", + " 1 34.481560 34.588249 34.726569 34.735903 33.140917 34.665190 \n", + " 2 29.574561 29.681299 29.819709 29.828989 28.233933 29.758262 \n", + " 3 39.540472 39.647137 39.785451 39.794800 38.199811 39.724085 \n", "\n", " 18 19 \n", "protein ion \n", - "protA 0 43.380650 43.407413 \n", - " 1 33.414868 33.441634 \n", - " 2 28.508008 28.534752 \n", - " 3 38.473762 38.500524 " + "protA 0 43.380650 43.407414 \n", + " 1 33.414869 33.441625 \n", + " 2 28.507947 28.534864 \n", + " 3 38.473758 38.500527 " ] }, "metadata": {}, @@ -779,94 +779,94 @@ " protA\n", " 0\n", " 44.602965\n", - " 44.474240\n", - " 41.489085\n", - " 43.216306\n", + " 44.474241\n", + " 41.489086\n", + " 43.216307\n", " 43.505708\n", - " 42.338405\n", + " 42.338404\n", " 43.454211\n", - " 43.102621\n", - " 41.897533\n", - " 43.625508\n", + " 43.102622\n", + " 41.897535\n", + " 43.625507\n", " 43.261340\n", - " 40.203346\n", + " 40.203349\n", " 44.447364\n", " 44.554027\n", " 44.692343\n", " 44.701690\n", " 43.106703\n", - " 44.630976\n", + " 44.630975\n", " 43.380650\n", - " 43.407413\n", + " 43.407414\n", " \n", " \n", " 1\n", - " 44.602971\n", - " 44.474230\n", - " 41.489107\n", - " 43.216313\n", - " 43.505686\n", - " 42.338402\n", - " 43.454200\n", - " 43.102617\n", - " 41.897521\n", - " 43.625514\n", - " 43.261352\n", - " 40.203317\n", - " 44.447358\n", - " 44.554025\n", - " 44.692351\n", - " 44.701697\n", - " 43.106711\n", - " 44.630983\n", - " 43.380648\n", - " 43.407414\n", + " 44.602972\n", + " 44.474249\n", + " 41.489073\n", + " 43.216315\n", + " 43.505703\n", + " 42.338413\n", + " 43.454197\n", + " 43.102620\n", + " 41.897512\n", + " 43.625505\n", + " 43.261331\n", + " 40.203391\n", + " 44.447346\n", + " 44.554035\n", + " 44.692355\n", + " 44.701690\n", + " 43.106704\n", + " 44.630976\n", + " 43.380655\n", + " 43.407411\n", " \n", " \n", " 2\n", - " 44.602957\n", - " 44.474255\n", - " 41.489023\n", - " 43.216293\n", - " 43.505823\n", - " 42.338464\n", - " 43.454188\n", - " 43.102600\n", - " 41.897529\n", - " 43.625595\n", - " 43.261344\n", - " 40.203515\n", - " 44.447308\n", - " 44.554114\n", - " 44.692426\n", - " 44.701652\n", - " 43.106771\n", - " 44.630949\n", - " 43.380667\n", - " 43.407411\n", + " 44.602906\n", + " 44.474240\n", + " 41.488883\n", + " 43.216364\n", + " 43.505720\n", + " 42.338528\n", + " 43.454296\n", + " 43.102677\n", + " 41.897604\n", + " 43.625475\n", + " 43.261341\n", + " 40.203474\n", + " 44.447231\n", + " 44.553969\n", + " 44.692378\n", + " 44.701658\n", + " 43.106603\n", + " 44.630931\n", + " 43.380617\n", + " 43.407534\n", " \n", " \n", " 3\n", - " 44.602965\n", + " 44.602964\n", " 44.474240\n", - " 41.489085\n", - " 43.216310\n", - " 43.505712\n", - " 42.338402\n", + " 41.489086\n", + " 43.216307\n", + " 43.505710\n", + " 42.338405\n", " 43.454213\n", - " 43.102623\n", - " 41.897535\n", - " 43.625505\n", + " 43.102622\n", + " 41.897527\n", + " 43.625508\n", " 43.261340\n", - " 40.203344\n", + " 40.203352\n", " 44.447363\n", " 44.554027\n", - " 44.692341\n", + " 44.692342\n", " 44.701690\n", - " 43.106701\n", - " 44.630973\n", - " 43.380653\n", - " 43.407414\n", + " 43.106702\n", + " 44.630975\n", + " 43.380648\n", + " 43.407417\n", " \n", " \n", "\n", @@ -875,31 +875,31 @@ "text/plain": [ " 0 1 2 3 4 5 \\\n", "protein ion \n", - "protA 0 44.602965 44.474240 41.489085 43.216306 43.505708 42.338405 \n", - " 1 44.602971 44.474230 41.489107 43.216313 43.505686 42.338402 \n", - " 2 44.602957 44.474255 41.489023 43.216293 43.505823 42.338464 \n", - " 3 44.602965 44.474240 41.489085 43.216310 43.505712 42.338402 \n", + "protA 0 44.602965 44.474241 41.489086 43.216307 43.505708 42.338404 \n", + " 1 44.602972 44.474249 41.489073 43.216315 43.505703 42.338413 \n", + " 2 44.602906 44.474240 41.488883 43.216364 43.505720 42.338528 \n", + " 3 44.602964 44.474240 41.489086 43.216307 43.505710 42.338405 \n", "\n", " 6 7 8 9 10 11 \\\n", "protein ion \n", - "protA 0 43.454211 43.102621 41.897533 43.625508 43.261340 40.203346 \n", - " 1 43.454200 43.102617 41.897521 43.625514 43.261352 40.203317 \n", - " 2 43.454188 43.102600 41.897529 43.625595 43.261344 40.203515 \n", - " 3 43.454213 43.102623 41.897535 43.625505 43.261340 40.203344 \n", + "protA 0 43.454211 43.102622 41.897535 43.625507 43.261340 40.203349 \n", + " 1 43.454197 43.102620 41.897512 43.625505 43.261331 40.203391 \n", + " 2 43.454296 43.102677 41.897604 43.625475 43.261341 40.203474 \n", + " 3 43.454213 43.102622 41.897527 43.625508 43.261340 40.203352 \n", "\n", " 12 13 14 15 16 17 \\\n", "protein ion \n", - "protA 0 44.447364 44.554027 44.692343 44.701690 43.106703 44.630976 \n", - " 1 44.447358 44.554025 44.692351 44.701697 43.106711 44.630983 \n", - " 2 44.447308 44.554114 44.692426 44.701652 43.106771 44.630949 \n", - " 3 44.447363 44.554027 44.692341 44.701690 43.106701 44.630973 \n", + "protA 0 44.447364 44.554027 44.692343 44.701690 43.106703 44.630975 \n", + " 1 44.447346 44.554035 44.692355 44.701690 43.106704 44.630976 \n", + " 2 44.447231 44.553969 44.692378 44.701658 43.106603 44.630931 \n", + " 3 44.447363 44.554027 44.692342 44.701690 43.106702 44.630975 \n", "\n", " 18 19 \n", "protein ion \n", - "protA 0 43.380650 43.407413 \n", - " 1 43.380648 43.407414 \n", - " 2 43.380667 43.407411 \n", - " 3 43.380653 43.407414 " + "protA 0 43.380650 43.407414 \n", + " 1 43.380655 43.407411 \n", + " 2 43.380617 43.407534 \n", + " 3 43.380648 43.407417 " ] }, "metadata": {}, @@ -944,15 +944,15 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2023-12-08 12:22:20,257 - directlfq.protein_intensity_estimation - INFO - 1 prots total\n", - "2023-12-08 12:22:20,258 - directlfq.protein_intensity_estimation - INFO - prot 0\n" + "2024-01-16 18:41:04,627 - directlfq.protein_intensity_estimation - INFO - 1 lfq-groups total\n", + "2024-01-16 18:41:04,631 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n" ] }, { @@ -1003,26 +1003,26 @@ " \n", " 0\n", " protA\n", - " 2.534980e+13\n", - " 2.318589e+13\n", - " 2.928181e+12\n", - " 9.695020e+12\n", - " 1.184861e+13\n", - " 5.275621e+12\n", - " 1.143313e+13\n", - " 8.960380e+12\n", - " 3.886496e+12\n", + " 2.550681e+13\n", + " 2.332953e+13\n", + " 2.946332e+12\n", + " 9.755077e+12\n", + " 1.192199e+13\n", + " 5.308341e+12\n", + " 1.150395e+13\n", + " 9.015887e+12\n", + " 3.910578e+12\n", " ...\n", - " 1.000241e+13\n", - " 1.201040e+12\n", - " 2.275799e+13\n", - " 2.450432e+13\n", - " 2.696994e+13\n", - " 2.714526e+13\n", - " 8.985770e+12\n", - " 2.584682e+13\n", - " 1.086479e+13\n", - " 1.106823e+13\n", + " 1.006437e+13\n", + " 1.208460e+12\n", + " 2.289902e+13\n", + " 2.465628e+13\n", + " 2.713699e+13\n", + " 2.731334e+13\n", + " 9.041394e+12\n", + " 2.600682e+13\n", + " 1.093207e+13\n", + " 1.113679e+13\n", " \n", " \n", "\n", @@ -1031,16 +1031,16 @@ ], "text/plain": [ " protein 0 1 2 3 \\\n", - "0 protA 2.534980e+13 2.318589e+13 2.928181e+12 9.695020e+12 \n", + "0 protA 2.550681e+13 2.332953e+13 2.946332e+12 9.755077e+12 \n", "\n", " 4 5 6 7 8 ... \\\n", - "0 1.184861e+13 5.275621e+12 1.143313e+13 8.960380e+12 3.886496e+12 ... \n", + "0 1.192199e+13 5.308341e+12 1.150395e+13 9.015887e+12 3.910578e+12 ... \n", "\n", " 10 11 12 13 14 \\\n", - "0 1.000241e+13 1.201040e+12 2.275799e+13 2.450432e+13 2.696994e+13 \n", + "0 1.006437e+13 1.208460e+12 2.289902e+13 2.465628e+13 2.713699e+13 \n", "\n", " 15 16 17 18 19 \n", - "0 2.714526e+13 8.985770e+12 2.584682e+13 1.086479e+13 1.106823e+13 \n", + "0 2.731334e+13 9.041394e+12 2.600682e+13 1.093207e+13 1.113679e+13 \n", "\n", "[1 rows x 21 columns]" ] @@ -1051,13 +1051,13 @@ { "data": { "text/plain": [ - "array([25349795642833.24, 23185890220888.97, 2928180586448.17,\n", - " 9695020357645.807, 11848609977072.47, 5275621107950.519,\n", - " 11433132923005.893, 8960379724734.42, 3886495984197.8735,\n", - " 12874540472742.57, 10002405236736.053, 1201039877802.1846,\n", - " 22757993614330.746, 24504324707272.664, 26969944908322.53,\n", - " 27145258441058.31, 8985769914714.105, 25846821137849.547,\n", - " 10864793434866.52, 11068226808633.043], dtype=object)" + "array([25506809860506.332, 23329533045893.477, 2946332363486.215,\n", + " 9755077268985.2, 11921993224575.64, 5308340747378.202,\n", + " 11503949328795.27, 9015887428968.75, 3910577876952.297,\n", + " 12954240952527.87, 10064371344868.074, 1208460069505.897,\n", + " 22899018922879.797, 24656284950204.83, 27136985048483.617,\n", + " 27313335493639.652, 9041394346226.639, 26006817726030.98,\n", + " 10932074976269.389, 11136794579192.637], dtype=object)" ] }, "metadata": {}, @@ -1090,15 +1090,15 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2023-12-08 12:26:12,022 - directlfq.protein_intensity_estimation - INFO - 4 prots total\n", - "2023-12-08 12:26:12,024 - directlfq.protein_intensity_estimation - INFO - prot 0\n" + "2024-01-16 18:41:04,681 - directlfq.protein_intensity_estimation - INFO - 4 lfq-groups total\n", + "2024-01-16 18:41:04,683 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n" ] }, { @@ -1149,98 +1149,98 @@ " \n", " 0\n", " protA\n", - " 2.531384e+13\n", - " 2.315286e+13\n", - " 2.924049e+12\n", - " 9.681216e+12\n", - " 1.183173e+13\n", - " 5.268128e+12\n", - " 1.141686e+13\n", - " 8.947613e+12\n", - " 3.880908e+12\n", + " 2.377121e+13\n", + " 2.174217e+13\n", + " 2.745890e+12\n", + " 9.091296e+12\n", + " 1.111070e+13\n", + " 4.947095e+12\n", + " 1.072115e+13\n", + " 8.402682e+12\n", + " 3.644466e+12\n", " ...\n", - " 9.988645e+12\n", - " 1.199318e+12\n", - " 2.272559e+13\n", - " 2.446956e+13\n", - " 2.693163e+13\n", - " 2.710675e+13\n", - " 8.972944e+12\n", - " 2.580999e+13\n", - " 1.084931e+13\n", - " 1.105253e+13\n", + " 9.379567e+12\n", + " 1.126250e+12\n", + " 2.134104e+13\n", + " 2.297854e+13\n", + " 2.529083e+13\n", + " 2.545478e+13\n", + " 8.426202e+12\n", + " 2.423725e+13\n", + " 1.018819e+13\n", + " 1.037897e+13\n", " \n", " \n", " 1\n", " protB\n", - " 8.906532e+11\n", - " 8.146271e+11\n", - " 1.028814e+11\n", - " 3.406308e+11\n", - " 4.162962e+11\n", - " 1.853563e+11\n", - " 4.016973e+11\n", - " 3.148190e+11\n", - " 1.365508e+11\n", + " 8.906542e+11\n", + " 8.146273e+11\n", + " 1.028809e+11\n", + " 3.406309e+11\n", + " 4.162956e+11\n", + " 1.853568e+11\n", + " 4.016985e+11\n", + " 3.148188e+11\n", + " 1.365504e+11\n", " ...\n", - " 3.514311e+11\n", - " 4.219781e+10\n", - " 7.995918e+11\n", - " 8.609472e+11\n", - " 9.475768e+11\n", - " 9.537363e+11\n", + " 3.514312e+11\n", + " 4.219766e+10\n", + " 7.995915e+11\n", + " 8.609485e+11\n", + " 9.475760e+11\n", + " 9.537380e+11\n", " 3.157105e+11\n", - " 9.081169e+11\n", - " 3.817282e+11\n", - " 3.888771e+11\n", + " 9.081165e+11\n", + " 3.817288e+11\n", + " 3.888777e+11\n", " \n", " \n", " 2\n", " protC\n", - " 8.906544e+11\n", - " 8.146285e+11\n", - " 1.028819e+11\n", - " 3.406296e+11\n", + " 8.906531e+11\n", + " 8.146276e+11\n", + " 1.028816e+11\n", + " 3.406301e+11\n", " 4.162955e+11\n", - " 1.853560e+11\n", - " 4.016979e+11\n", - " 3.148195e+11\n", - " 1.365506e+11\n", + " 1.853571e+11\n", + " 4.016981e+11\n", + " 3.148193e+11\n", + " 1.365502e+11\n", " ...\n", - " 3.514307e+11\n", - " 4.219777e+10\n", - " 7.995936e+11\n", - " 8.609486e+11\n", - " 9.475759e+11\n", - " 9.537344e+11\n", - " 3.157112e+11\n", - " 9.081153e+11\n", - " 3.817297e+11\n", - " 3.888760e+11\n", + " 3.514310e+11\n", + " 4.219813e+10\n", + " 7.995913e+11\n", + " 8.609496e+11\n", + " 9.475767e+11\n", + " 9.537349e+11\n", + " 3.157113e+11\n", + " 9.081163e+11\n", + " 3.817300e+11\n", + " 3.888769e+11\n", " \n", " \n", " 3\n", " protD\n", - " 2.671963e+12\n", - " 2.443884e+12\n", - " 3.086451e+11\n", - " 1.021892e+12\n", - " 1.248886e+12\n", - " 5.560711e+11\n", - " 1.205096e+12\n", - " 9.444586e+11\n", - " 4.096517e+11\n", + " 2.671962e+12\n", + " 2.443883e+12\n", + " 3.086453e+11\n", + " 1.021890e+12\n", + " 1.248887e+12\n", + " 5.560694e+11\n", + " 1.205094e+12\n", + " 9.444571e+11\n", + " 4.096502e+11\n", " ...\n", - " 1.054292e+12\n", + " 1.054291e+12\n", " 1.265943e+11\n", - " 2.398774e+12\n", - " 2.582846e+12\n", - " 2.842730e+12\n", - " 2.861209e+12\n", - " 9.471320e+11\n", - " 2.724343e+12\n", - " 1.145188e+12\n", - " 1.166632e+12\n", + " 2.398776e+12\n", + " 2.582841e+12\n", + " 2.842731e+12\n", + " 2.861211e+12\n", + " 9.471338e+11\n", + " 2.724346e+12\n", + " 1.145189e+12\n", + " 1.166631e+12\n", " \n", " \n", "\n", @@ -1249,28 +1249,28 @@ ], "text/plain": [ " protein 0 1 2 3 \\\n", - "0 protA 2.531384e+13 2.315286e+13 2.924049e+12 9.681216e+12 \n", - "1 protB 8.906532e+11 8.146271e+11 1.028814e+11 3.406308e+11 \n", - "2 protC 8.906544e+11 8.146285e+11 1.028819e+11 3.406296e+11 \n", - "3 protD 2.671963e+12 2.443884e+12 3.086451e+11 1.021892e+12 \n", + "0 protA 2.377121e+13 2.174217e+13 2.745890e+12 9.091296e+12 \n", + "1 protB 8.906542e+11 8.146273e+11 1.028809e+11 3.406309e+11 \n", + "2 protC 8.906531e+11 8.146276e+11 1.028816e+11 3.406301e+11 \n", + "3 protD 2.671962e+12 2.443883e+12 3.086453e+11 1.021890e+12 \n", "\n", " 4 5 6 7 8 ... \\\n", - "0 1.183173e+13 5.268128e+12 1.141686e+13 8.947613e+12 3.880908e+12 ... \n", - "1 4.162962e+11 1.853563e+11 4.016973e+11 3.148190e+11 1.365508e+11 ... \n", - "2 4.162955e+11 1.853560e+11 4.016979e+11 3.148195e+11 1.365506e+11 ... \n", - "3 1.248886e+12 5.560711e+11 1.205096e+12 9.444586e+11 4.096517e+11 ... \n", + "0 1.111070e+13 4.947095e+12 1.072115e+13 8.402682e+12 3.644466e+12 ... \n", + "1 4.162956e+11 1.853568e+11 4.016985e+11 3.148188e+11 1.365504e+11 ... \n", + "2 4.162955e+11 1.853571e+11 4.016981e+11 3.148193e+11 1.365502e+11 ... \n", + "3 1.248887e+12 5.560694e+11 1.205094e+12 9.444571e+11 4.096502e+11 ... \n", "\n", " 10 11 12 13 14 \\\n", - "0 9.988645e+12 1.199318e+12 2.272559e+13 2.446956e+13 2.693163e+13 \n", - "1 3.514311e+11 4.219781e+10 7.995918e+11 8.609472e+11 9.475768e+11 \n", - "2 3.514307e+11 4.219777e+10 7.995936e+11 8.609486e+11 9.475759e+11 \n", - "3 1.054292e+12 1.265943e+11 2.398774e+12 2.582846e+12 2.842730e+12 \n", + "0 9.379567e+12 1.126250e+12 2.134104e+13 2.297854e+13 2.529083e+13 \n", + "1 3.514312e+11 4.219766e+10 7.995915e+11 8.609485e+11 9.475760e+11 \n", + "2 3.514310e+11 4.219813e+10 7.995913e+11 8.609496e+11 9.475767e+11 \n", + "3 1.054291e+12 1.265943e+11 2.398776e+12 2.582841e+12 2.842731e+12 \n", "\n", " 15 16 17 18 19 \n", - "0 2.710675e+13 8.972944e+12 2.580999e+13 1.084931e+13 1.105253e+13 \n", - "1 9.537363e+11 3.157105e+11 9.081169e+11 3.817282e+11 3.888771e+11 \n", - "2 9.537344e+11 3.157112e+11 9.081153e+11 3.817297e+11 3.888760e+11 \n", - "3 2.861209e+12 9.471320e+11 2.724343e+12 1.145188e+12 1.166632e+12 \n", + "0 2.545478e+13 8.426202e+12 2.423725e+13 1.018819e+13 1.037897e+13 \n", + "1 9.537380e+11 3.157105e+11 9.081165e+11 3.817288e+11 3.888777e+11 \n", + "2 9.537349e+11 3.157113e+11 9.081163e+11 3.817300e+11 3.888769e+11 \n", + "3 2.861211e+12 9.471338e+11 2.724346e+12 1.145189e+12 1.166631e+12 \n", "\n", "[4 rows x 21 columns]" ] @@ -1303,6 +1303,34 @@ "\n" ] }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [], + "source": [ + "import directlfq.protein_intensity_estimation as lfq_intensity_estimation\n", + "\n", + "def test_nameswitch_indices_are_recovered_correctly():\n", + " # Example usage\n", + " array = np.array(['a', 'a', 'a', 'b', 'c', 'c', 'd'])\n", + " start_indices = lfq_intensity_estimation.find_nameswitch_indices(array)\n", + "\n", + " assert (array[start_indices[0]:start_indices[1]] == 'a').all()\n", + " assert len(array[start_indices[0]:start_indices[1]]) == 3\n", + "\n", + " assert (array[start_indices[1]:start_indices[2]] == 'b').all()\n", + " assert len(array[start_indices[1]:start_indices[2]]) == 1\n", + "\n", + " assert (array[start_indices[2]:start_indices[3]] == 'c').all()\n", + " assert len(array[start_indices[2]:start_indices[3]]) == 2\n", + "\n", + " assert (array[start_indices[3]:start_indices[4]] == 'd').all()\n", + " assert len(array[start_indices[3]:start_indices[4]]) == 1\n", + "\n", + "test_nameswitch_indices_are_recovered_correctly()" + ] + }, { "cell_type": "markdown", "metadata": {}, @@ -1312,7 +1340,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ @@ -1333,7 +1361,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": {}, "outputs": [ { @@ -1407,7 +1435,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": {}, "outputs": [], "source": [ @@ -1423,7 +1451,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "metadata": {}, "outputs": [ { @@ -1501,7 +1529,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 11, "metadata": {}, "outputs": [], "source": [ @@ -1516,7 +1544,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "metadata": {}, "outputs": [ { @@ -1554,6 +1582,18 @@ "display_name": "alphatemplate", "language": "python", "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.17" } }, "nbformat": 4, From 55a6c3276468794432f43ab4f3588a9010b08db3 Mon Sep 17 00:00:00 2001 From: ammarcsj <70114795+ammarcsj@users.noreply.github.com> Date: Tue, 16 Jan 2024 18:47:24 +0100 Subject: [PATCH 4/8] add --- .../derive_precursors_diapasef_diann.ipynb | 733 ++++++++++++++++++ 1 file changed, 733 insertions(+) create mode 100644 tests/ratio_tests/derive_precursors_diapasef_diann.ipynb diff --git a/tests/ratio_tests/derive_precursors_diapasef_diann.ipynb b/tests/ratio_tests/derive_precursors_diapasef_diann.ipynb new file mode 100644 index 0000000..df4c0f6 --- /dev/null +++ b/tests/ratio_tests/derive_precursors_diapasef_diann.ipynb @@ -0,0 +1,733 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "INPUT_FILE = \"../../test_data/system_tests/diaPASEF_diann/report.tsv.top3added.tsv.precursorgrouping.diann_fragion_isotopes.aq_reformat.tsv\"\n", + "INPUT_FILE = \"../../test_data/system_tests/diaPASEF_diann/report.tsv.top3added.tsv.precursorgrouping.shortened.diann_fragion_isotopes.aq_reformat.tsv\"\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2024-01-16 18:14:17,175 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:14:18,093 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:14:19,390 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:14:19,431 - directlfq.protein_intensity_estimation - INFO - 24995 lfq-objects total\n", + "2024-01-16 18:14:25,811 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:14:25,870 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", + "2024-01-16 18:14:26,918 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:28,042 - directlfq.protein_intensity_estimation - INFO - lfq-object 2500\n", + "2024-01-16 18:14:28,091 - directlfq.protein_intensity_estimation - INFO - lfq-object 100\n", + "2024-01-16 18:14:28,110 - directlfq.protein_intensity_estimation - INFO - lfq-object 1300\n", + "2024-01-16 18:14:28,121 - directlfq.protein_intensity_estimation - INFO - lfq-object 1900\n", + "2024-01-16 18:14:28,122 - directlfq.protein_intensity_estimation - INFO - lfq-object 700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:29,160 - directlfq.protein_intensity_estimation - INFO - lfq-object 200\n", + "2024-01-16 18:14:29,210 - directlfq.protein_intensity_estimation - INFO - lfq-object 800\n", + "2024-01-16 18:14:29,218 - directlfq.protein_intensity_estimation - INFO - lfq-object 1400\n", + "2024-01-16 18:14:29,219 - directlfq.protein_intensity_estimation - INFO - lfq-object 2000\n", + "2024-01-16 18:14:29,268 - directlfq.protein_intensity_estimation - INFO - lfq-object 2600\n", + "2024-01-16 18:14:29,679 - directlfq.protein_intensity_estimation - INFO - lfq-object 3200\n", + "2024-01-16 18:14:29,697 - directlfq.protein_intensity_estimation - INFO - lfq-object 3800\n", + "2024-01-16 18:14:29,727 - directlfq.protein_intensity_estimation - INFO - lfq-object 5000\n", + "2024-01-16 18:14:29,750 - directlfq.protein_intensity_estimation - INFO - lfq-object 4400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:30,416 - directlfq.protein_intensity_estimation - INFO - lfq-object 300\n", + "2024-01-16 18:14:30,463 - directlfq.protein_intensity_estimation - INFO - lfq-object 2100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:30,488 - directlfq.protein_intensity_estimation - INFO - lfq-object 900\n", + "2024-01-16 18:14:30,498 - directlfq.protein_intensity_estimation - INFO - lfq-object 1500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:30,649 - directlfq.protein_intensity_estimation - INFO - lfq-object 2700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:30,956 - directlfq.protein_intensity_estimation - INFO - lfq-object 3300\n", + "2024-01-16 18:14:30,962 - directlfq.protein_intensity_estimation - INFO - lfq-object 3900\n", + "2024-01-16 18:14:31,028 - directlfq.protein_intensity_estimation - INFO - lfq-object 4500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:31,122 - directlfq.protein_intensity_estimation - INFO - lfq-object 5100\n", + "2024-01-16 18:14:31,183 - directlfq.protein_intensity_estimation - INFO - lfq-object 5700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:31,766 - directlfq.protein_intensity_estimation - INFO - lfq-object 400\n", + "2024-01-16 18:14:31,773 - directlfq.protein_intensity_estimation - INFO - lfq-object 2200\n", + "2024-01-16 18:14:31,778 - directlfq.protein_intensity_estimation - INFO - lfq-object 1600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:31,810 - directlfq.protein_intensity_estimation - INFO - lfq-object 1000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:31,909 - directlfq.protein_intensity_estimation - INFO - lfq-object 2800\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:32,174 - directlfq.protein_intensity_estimation - INFO - lfq-object 4000\n", + "2024-01-16 18:14:32,281 - directlfq.protein_intensity_estimation - INFO - lfq-object 3400\n", + "2024-01-16 18:14:32,332 - directlfq.protein_intensity_estimation - INFO - lfq-object 4600\n", + "2024-01-16 18:14:32,353 - directlfq.protein_intensity_estimation - INFO - lfq-object 5200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:32,437 - directlfq.protein_intensity_estimation - INFO - lfq-object 5800\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:32,963 - directlfq.protein_intensity_estimation - INFO - lfq-object 1100\n", + "2024-01-16 18:14:32,990 - directlfq.protein_intensity_estimation - INFO - lfq-object 500\n", + "2024-01-16 18:14:33,009 - directlfq.protein_intensity_estimation - INFO - lfq-object 1700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:33,149 - directlfq.protein_intensity_estimation - INFO - lfq-object 2300\n", + "2024-01-16 18:14:33,210 - directlfq.protein_intensity_estimation - INFO - lfq-object 2900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:33,406 - directlfq.protein_intensity_estimation - INFO - lfq-object 4100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:33,547 - directlfq.protein_intensity_estimation - INFO - lfq-object 3500\n", + "2024-01-16 18:14:33,564 - directlfq.protein_intensity_estimation - INFO - lfq-object 5300\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:33,606 - directlfq.protein_intensity_estimation - INFO - lfq-object 4700\n", + "2024-01-16 18:14:33,673 - directlfq.protein_intensity_estimation - INFO - lfq-object 5900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:34,229 - directlfq.protein_intensity_estimation - INFO - lfq-object 1200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:34,278 - directlfq.protein_intensity_estimation - INFO - lfq-object 1800\n", + "2024-01-16 18:14:34,281 - directlfq.protein_intensity_estimation - INFO - lfq-object 600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:34,401 - directlfq.protein_intensity_estimation - INFO - lfq-object 2400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:34,470 - directlfq.protein_intensity_estimation - INFO - lfq-object 3000\n", + "2024-01-16 18:14:34,706 - directlfq.protein_intensity_estimation - INFO - lfq-object 4200\n", + "2024-01-16 18:14:34,760 - directlfq.protein_intensity_estimation - INFO - lfq-object 3600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:34,819 - directlfq.protein_intensity_estimation - INFO - lfq-object 4800\n", + "2024-01-16 18:14:34,855 - directlfq.protein_intensity_estimation - INFO - lfq-object 5400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:34,912 - directlfq.protein_intensity_estimation - INFO - lfq-object 6000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:35,706 - directlfq.protein_intensity_estimation - INFO - lfq-object 3100\n", + "2024-01-16 18:14:35,734 - directlfq.protein_intensity_estimation - INFO - lfq-object 6300\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:35,887 - directlfq.protein_intensity_estimation - INFO - lfq-object 4300\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:36,027 - directlfq.protein_intensity_estimation - INFO - lfq-object 3700\n", + "2024-01-16 18:14:36,030 - directlfq.protein_intensity_estimation - INFO - lfq-object 4900\n", + "2024-01-16 18:14:36,042 - directlfq.protein_intensity_estimation - INFO - lfq-object 5500\n", + "2024-01-16 18:14:36,129 - directlfq.protein_intensity_estimation - INFO - lfq-object 6100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:36,468 - directlfq.protein_intensity_estimation - INFO - lfq-object 6900\n", + "2024-01-16 18:14:36,647 - directlfq.protein_intensity_estimation - INFO - lfq-object 7500\n", + "2024-01-16 18:14:36,796 - directlfq.protein_intensity_estimation - INFO - lfq-object 6400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:37,113 - directlfq.protein_intensity_estimation - INFO - lfq-object 5600\n", + "2024-01-16 18:14:37,195 - directlfq.protein_intensity_estimation - INFO - lfq-object 6200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:37,515 - directlfq.protein_intensity_estimation - INFO - lfq-object 7000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:37,708 - directlfq.protein_intensity_estimation - INFO - lfq-object 7600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:37,840 - directlfq.protein_intensity_estimation - INFO - lfq-object 6500\n", + "2024-01-16 18:14:38,221 - directlfq.protein_intensity_estimation - INFO - lfq-object 8200\n", + "2024-01-16 18:14:38,352 - directlfq.protein_intensity_estimation - INFO - lfq-object 8800\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:38,505 - directlfq.protein_intensity_estimation - INFO - lfq-object 9400\n", + "2024-01-16 18:14:38,554 - directlfq.protein_intensity_estimation - INFO - lfq-object 7100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:38,744 - directlfq.protein_intensity_estimation - INFO - lfq-object 7700\n", + "2024-01-16 18:14:38,892 - directlfq.protein_intensity_estimation - INFO - lfq-object 6600\n", + "2024-01-16 18:14:38,993 - directlfq.protein_intensity_estimation - INFO - lfq-object 10000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:39,348 - directlfq.protein_intensity_estimation - INFO - lfq-object 8300\n", + "2024-01-16 18:14:39,446 - directlfq.protein_intensity_estimation - INFO - lfq-object 8900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:39,622 - directlfq.protein_intensity_estimation - INFO - lfq-object 9500\n", + "2024-01-16 18:14:39,691 - directlfq.protein_intensity_estimation - INFO - lfq-object 7200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:39,816 - directlfq.protein_intensity_estimation - INFO - lfq-object 7800\n", + "2024-01-16 18:14:40,097 - directlfq.protein_intensity_estimation - INFO - lfq-object 6700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:40,146 - directlfq.protein_intensity_estimation - INFO - lfq-object 10100\n", + "2024-01-16 18:14:40,207 - directlfq.protein_intensity_estimation - INFO - lfq-object 10700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:40,365 - directlfq.protein_intensity_estimation - INFO - lfq-object 11300\n", + "2024-01-16 18:14:40,377 - directlfq.protein_intensity_estimation - INFO - lfq-object 11900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:40,580 - directlfq.protein_intensity_estimation - INFO - lfq-object 8400\n", + "2024-01-16 18:14:40,698 - directlfq.protein_intensity_estimation - INFO - lfq-object 9000\n", + "2024-01-16 18:14:40,936 - directlfq.protein_intensity_estimation - INFO - lfq-object 7300\n", + "2024-01-16 18:14:40,942 - directlfq.protein_intensity_estimation - INFO - lfq-object 9600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:41,101 - directlfq.protein_intensity_estimation - INFO - lfq-object 7900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:41,456 - directlfq.protein_intensity_estimation - INFO - lfq-object 10200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:41,592 - directlfq.protein_intensity_estimation - INFO - lfq-object 10800\n", + "2024-01-16 18:14:41,616 - directlfq.protein_intensity_estimation - INFO - lfq-object 11400\n", + "2024-01-16 18:14:41,670 - directlfq.protein_intensity_estimation - INFO - lfq-object 12000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:41,854 - directlfq.protein_intensity_estimation - INFO - lfq-object 6800\n", + "2024-01-16 18:14:41,895 - directlfq.protein_intensity_estimation - INFO - lfq-object 8500\n", + "2024-01-16 18:14:41,918 - directlfq.protein_intensity_estimation - INFO - lfq-object 9100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:42,241 - directlfq.protein_intensity_estimation - INFO - lfq-object 7400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:42,275 - directlfq.protein_intensity_estimation - INFO - lfq-object 9700\n", + "2024-01-16 18:14:42,307 - directlfq.protein_intensity_estimation - INFO - lfq-object 8000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:42,759 - directlfq.protein_intensity_estimation - INFO - lfq-object 10300\n", + "2024-01-16 18:14:42,848 - directlfq.protein_intensity_estimation - INFO - lfq-object 10900\n", + "2024-01-16 18:14:42,862 - directlfq.protein_intensity_estimation - INFO - lfq-object 11500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:43,043 - directlfq.protein_intensity_estimation - INFO - lfq-object 12100\n", + "2024-01-16 18:14:43,148 - directlfq.protein_intensity_estimation - INFO - lfq-object 9200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:43,182 - directlfq.protein_intensity_estimation - INFO - lfq-object 8600\n", + "2024-01-16 18:14:43,232 - directlfq.protein_intensity_estimation - INFO - lfq-object 12500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:43,553 - directlfq.protein_intensity_estimation - INFO - lfq-object 9800\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:44,062 - directlfq.protein_intensity_estimation - INFO - lfq-object 10400\n", + "2024-01-16 18:14:44,123 - directlfq.protein_intensity_estimation - INFO - lfq-object 8100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:44,147 - directlfq.protein_intensity_estimation - INFO - lfq-object 11600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:44,299 - directlfq.protein_intensity_estimation - INFO - lfq-object 11000\n", + "2024-01-16 18:14:44,314 - directlfq.protein_intensity_estimation - INFO - lfq-object 12200\n", + "2024-01-16 18:14:44,425 - directlfq.protein_intensity_estimation - INFO - lfq-object 9300\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:44,483 - directlfq.protein_intensity_estimation - INFO - lfq-object 12600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:44,822 - directlfq.protein_intensity_estimation - INFO - lfq-object 9900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:45,015 - directlfq.protein_intensity_estimation - INFO - lfq-object 8700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:45,380 - directlfq.protein_intensity_estimation - INFO - lfq-object 11700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:45,419 - directlfq.protein_intensity_estimation - INFO - lfq-object 10500\n", + "2024-01-16 18:14:45,453 - directlfq.protein_intensity_estimation - INFO - lfq-object 13200\n", + "2024-01-16 18:14:45,616 - directlfq.protein_intensity_estimation - INFO - lfq-object 12300\n", + "2024-01-16 18:14:45,635 - directlfq.protein_intensity_estimation - INFO - lfq-object 11100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:45,815 - directlfq.protein_intensity_estimation - INFO - lfq-object 12700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:46,292 - directlfq.protein_intensity_estimation - INFO - lfq-object 13800\n", + "2024-01-16 18:14:46,438 - directlfq.protein_intensity_estimation - INFO - lfq-object 14400\n", + "2024-01-16 18:14:46,768 - directlfq.protein_intensity_estimation - INFO - lfq-object 13300\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:46,794 - directlfq.protein_intensity_estimation - INFO - lfq-object 15000\n", + "2024-01-16 18:14:46,977 - directlfq.protein_intensity_estimation - INFO - lfq-object 12400\n", + "2024-01-16 18:14:47,132 - directlfq.protein_intensity_estimation - INFO - lfq-object 12800\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:47,254 - directlfq.protein_intensity_estimation - INFO - lfq-object 11800\n", + "2024-01-16 18:14:47,258 - directlfq.protein_intensity_estimation - INFO - lfq-object 10600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:47,450 - directlfq.protein_intensity_estimation - INFO - lfq-object 11200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:47,538 - directlfq.protein_intensity_estimation - INFO - lfq-object 13900\n", + "2024-01-16 18:14:47,756 - directlfq.protein_intensity_estimation - INFO - lfq-object 14500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:48,082 - directlfq.protein_intensity_estimation - INFO - lfq-object 15100\n", + "2024-01-16 18:14:48,103 - directlfq.protein_intensity_estimation - INFO - lfq-object 13400\n", + "2024-01-16 18:14:48,355 - directlfq.protein_intensity_estimation - INFO - lfq-object 15700\n", + "2024-01-16 18:14:48,427 - directlfq.protein_intensity_estimation - INFO - lfq-object 12900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:48,770 - directlfq.protein_intensity_estimation - INFO - lfq-object 16300\n", + "2024-01-16 18:14:48,861 - directlfq.protein_intensity_estimation - INFO - lfq-object 14000\n", + "2024-01-16 18:14:49,023 - directlfq.protein_intensity_estimation - INFO - lfq-object 14600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:49,236 - directlfq.protein_intensity_estimation - INFO - lfq-object 15200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:49,323 - directlfq.protein_intensity_estimation - INFO - lfq-object 13500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:49,509 - directlfq.protein_intensity_estimation - INFO - lfq-object 15800\n", + "2024-01-16 18:14:49,534 - directlfq.protein_intensity_estimation - INFO - lfq-object 13000\n", + "2024-01-16 18:14:49,529 - directlfq.protein_intensity_estimation - INFO - lfq-object 16900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:49,777 - directlfq.protein_intensity_estimation - INFO - lfq-object 17500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:49,874 - directlfq.protein_intensity_estimation - INFO - lfq-object 16400\n", + "2024-01-16 18:14:49,968 - directlfq.protein_intensity_estimation - INFO - lfq-object 14100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:50,180 - directlfq.protein_intensity_estimation - INFO - lfq-object 14700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:50,476 - directlfq.protein_intensity_estimation - INFO - lfq-object 15300\n", + "2024-01-16 18:14:50,497 - directlfq.protein_intensity_estimation - INFO - lfq-object 13600\n", + "2024-01-16 18:14:50,753 - directlfq.protein_intensity_estimation - INFO - lfq-object 13100\n", + "2024-01-16 18:14:50,776 - directlfq.protein_intensity_estimation - INFO - lfq-object 17000\n", + "2024-01-16 18:14:50,812 - directlfq.protein_intensity_estimation - INFO - lfq-object 15900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:50,999 - directlfq.protein_intensity_estimation - INFO - lfq-object 17600\n", + "2024-01-16 18:14:51,055 - directlfq.protein_intensity_estimation - INFO - lfq-object 18200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:51,193 - directlfq.protein_intensity_estimation - INFO - lfq-object 16500\n", + "2024-01-16 18:14:51,277 - directlfq.protein_intensity_estimation - INFO - lfq-object 14200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:51,500 - directlfq.protein_intensity_estimation - INFO - lfq-object 14800\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:51,748 - directlfq.protein_intensity_estimation - INFO - lfq-object 13700\n", + "2024-01-16 18:14:51,777 - directlfq.protein_intensity_estimation - INFO - lfq-object 15400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:52,183 - directlfq.protein_intensity_estimation - INFO - lfq-object 17100\n", + "2024-01-16 18:14:52,176 - directlfq.protein_intensity_estimation - INFO - lfq-object 16000\n", + "2024-01-16 18:14:52,245 - directlfq.protein_intensity_estimation - INFO - lfq-object 18800\n", + "2024-01-16 18:14:52,341 - directlfq.protein_intensity_estimation - INFO - lfq-object 17700\n", + "2024-01-16 18:14:52,448 - directlfq.protein_intensity_estimation - INFO - lfq-object 18300\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:52,565 - directlfq.protein_intensity_estimation - INFO - lfq-object 16600\n", + "2024-01-16 18:14:52,585 - directlfq.protein_intensity_estimation - INFO - lfq-object 14300\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:52,888 - directlfq.protein_intensity_estimation - INFO - lfq-object 14900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:53,152 - directlfq.protein_intensity_estimation - INFO - lfq-object 15500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:53,259 - directlfq.protein_intensity_estimation - INFO - lfq-object 19400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:53,475 - directlfq.protein_intensity_estimation - INFO - lfq-object 16100\n", + "2024-01-16 18:14:53,489 - directlfq.protein_intensity_estimation - INFO - lfq-object 17200\n", + "2024-01-16 18:14:53,572 - directlfq.protein_intensity_estimation - INFO - lfq-object 18900\n", + "2024-01-16 18:14:53,710 - directlfq.protein_intensity_estimation - INFO - lfq-object 17800\n", + "2024-01-16 18:14:53,790 - directlfq.protein_intensity_estimation - INFO - lfq-object 18400\n", + "2024-01-16 18:14:53,841 - directlfq.protein_intensity_estimation - INFO - lfq-object 16700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:53,954 - directlfq.protein_intensity_estimation - INFO - lfq-object 20000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:54,479 - directlfq.protein_intensity_estimation - INFO - lfq-object 15600\n", + "2024-01-16 18:14:54,525 - directlfq.protein_intensity_estimation - INFO - lfq-object 19500\n", + "2024-01-16 18:14:54,769 - directlfq.protein_intensity_estimation - INFO - lfq-object 17300\n", + "2024-01-16 18:14:54,790 - directlfq.protein_intensity_estimation - INFO - lfq-object 16200\n", + "2024-01-16 18:14:54,833 - directlfq.protein_intensity_estimation - INFO - lfq-object 19000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:55,081 - directlfq.protein_intensity_estimation - INFO - lfq-object 17900\n", + "2024-01-16 18:14:55,135 - directlfq.protein_intensity_estimation - INFO - lfq-object 18500\n", + "2024-01-16 18:14:55,134 - directlfq.protein_intensity_estimation - INFO - lfq-object 16800\n", + "2024-01-16 18:14:55,230 - directlfq.protein_intensity_estimation - INFO - lfq-object 20100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:55,667 - directlfq.protein_intensity_estimation - INFO - lfq-object 20700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:55,863 - directlfq.protein_intensity_estimation - INFO - lfq-object 19600\n", + "2024-01-16 18:14:55,876 - directlfq.protein_intensity_estimation - INFO - lfq-object 21300\n", + "2024-01-16 18:14:56,063 - directlfq.protein_intensity_estimation - INFO - lfq-object 17400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:56,281 - directlfq.protein_intensity_estimation - INFO - lfq-object 21900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:56,469 - directlfq.protein_intensity_estimation - INFO - lfq-object 18000\n", + "2024-01-16 18:14:56,514 - directlfq.protein_intensity_estimation - INFO - lfq-object 18600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:56,653 - directlfq.protein_intensity_estimation - INFO - lfq-object 20200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:56,722 - directlfq.protein_intensity_estimation - INFO - lfq-object 19100\n", + "2024-01-16 18:14:56,996 - directlfq.protein_intensity_estimation - INFO - lfq-object 20800\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:57,176 - directlfq.protein_intensity_estimation - INFO - lfq-object 21400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:57,307 - directlfq.protein_intensity_estimation - INFO - lfq-object 22500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:57,501 - directlfq.protein_intensity_estimation - INFO - lfq-object 22000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:57,704 - directlfq.protein_intensity_estimation - INFO - lfq-object 19700\n", + "2024-01-16 18:14:57,775 - directlfq.protein_intensity_estimation - INFO - lfq-object 18700\n", + "2024-01-16 18:14:57,829 - directlfq.protein_intensity_estimation - INFO - lfq-object 18100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:58,047 - directlfq.protein_intensity_estimation - INFO - lfq-object 19200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:58,484 - directlfq.protein_intensity_estimation - INFO - lfq-object 20300\n", + "2024-01-16 18:14:58,550 - directlfq.protein_intensity_estimation - INFO - lfq-object 21500\n", + "2024-01-16 18:14:58,562 - directlfq.protein_intensity_estimation - INFO - lfq-object 22600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:58,801 - directlfq.protein_intensity_estimation - INFO - lfq-object 23200\n", + "2024-01-16 18:14:58,912 - directlfq.protein_intensity_estimation - INFO - lfq-object 20900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:58,938 - directlfq.protein_intensity_estimation - INFO - lfq-object 22100\n", + "2024-01-16 18:14:59,015 - directlfq.protein_intensity_estimation - INFO - lfq-object 19800\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:59,215 - directlfq.protein_intensity_estimation - INFO - lfq-object 23800\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:59,309 - directlfq.protein_intensity_estimation - INFO - lfq-object 19300\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:14:59,507 - directlfq.protein_intensity_estimation - INFO - lfq-object 24400\n", + "2024-01-16 18:14:59,719 - directlfq.protein_intensity_estimation - INFO - lfq-object 22700\n", + "2024-01-16 18:14:59,806 - directlfq.protein_intensity_estimation - INFO - lfq-object 20400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:00,037 - directlfq.protein_intensity_estimation - INFO - lfq-object 23300\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:00,212 - directlfq.protein_intensity_estimation - INFO - lfq-object 21600\n", + "2024-01-16 18:15:00,263 - directlfq.protein_intensity_estimation - INFO - lfq-object 21000\n", + "2024-01-16 18:15:00,295 - directlfq.protein_intensity_estimation - INFO - lfq-object 19900\n", + "2024-01-16 18:15:00,491 - directlfq.protein_intensity_estimation - INFO - lfq-object 23900\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:00,710 - directlfq.protein_intensity_estimation - INFO - lfq-object 22200\n", + "2024-01-16 18:15:00,746 - directlfq.protein_intensity_estimation - INFO - lfq-object 24500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:01,029 - directlfq.protein_intensity_estimation - INFO - lfq-object 20500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:01,389 - directlfq.protein_intensity_estimation - INFO - lfq-object 22800\n", + "2024-01-16 18:15:01,441 - directlfq.protein_intensity_estimation - INFO - lfq-object 21700\n", + "2024-01-16 18:15:01,454 - directlfq.protein_intensity_estimation - INFO - lfq-object 21100\n", + "2024-01-16 18:15:01,627 - directlfq.protein_intensity_estimation - INFO - lfq-object 24000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:01,718 - directlfq.protein_intensity_estimation - INFO - lfq-object 23400\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:01,839 - directlfq.protein_intensity_estimation - INFO - lfq-object 22300\n", + "2024-01-16 18:15:01,914 - directlfq.protein_intensity_estimation - INFO - lfq-object 24600\n", + "2024-01-16 18:15:02,125 - directlfq.protein_intensity_estimation - INFO - lfq-object 20600\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:02,507 - directlfq.protein_intensity_estimation - INFO - lfq-object 22900\n", + "2024-01-16 18:15:02,527 - directlfq.protein_intensity_estimation - INFO - lfq-object 21800\n", + "2024-01-16 18:15:02,610 - directlfq.protein_intensity_estimation - INFO - lfq-object 21200\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:02,807 - directlfq.protein_intensity_estimation - INFO - lfq-object 23500\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:02,871 - directlfq.protein_intensity_estimation - INFO - lfq-object 22400\n", + "2024-01-16 18:15:03,097 - directlfq.protein_intensity_estimation - INFO - lfq-object 24100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:03,379 - directlfq.protein_intensity_estimation - INFO - lfq-object 24700\n", + "2024-01-16 18:15:03,552 - directlfq.protein_intensity_estimation - INFO - lfq-object 23000\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:03,843 - directlfq.protein_intensity_estimation - INFO - lfq-object 23600\n", + "2024-01-16 18:15:04,137 - directlfq.protein_intensity_estimation - INFO - lfq-object 24200\n", + "2024-01-16 18:15:04,403 - directlfq.protein_intensity_estimation - INFO - lfq-object 24800\n", + "2024-01-16 18:15:04,587 - directlfq.protein_intensity_estimation - INFO - lfq-object 23100\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:04,858 - directlfq.protein_intensity_estimation - INFO - lfq-object 23700\n", + "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", + " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:15:05,156 - directlfq.protein_intensity_estimation - INFO - lfq-object 24300\n", + "2024-01-16 18:15:05,422 - directlfq.protein_intensity_estimation - INFO - lfq-object 24900\n", + "2024-01-16 18:15:08,308 - directlfq.lfq_manager - INFO - Could not add additional columns to protein table, printing without additional columns.\n", + "2024-01-16 18:15:08,309 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:15:11,738 - directlfq.lfq_manager - INFO - Analysis finished!\n" + ] + } + ], + "source": [ + "import directlfq.lfq_manager as lfq_manager\n", + "\n", + "lfq_manager.run_lfq(INPUT_FILE, num_cores=10)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "directlfq", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.17" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} From f11405a05421907f5e185f7d42ff7a3ada6bb964 Mon Sep 17 00:00:00 2001 From: ammarcsj <70114795+ammarcsj@users.noreply.github.com> Date: Tue, 16 Jan 2024 18:47:31 +0100 Subject: [PATCH 5/8] re-run --- ...n_pipeline_w_different_input_formats.ipynb | 218 ++-- .../ratio_tests/compare_diapasef_diann.ipynb | 1074 +++++++++-------- 2 files changed, 677 insertions(+), 615 deletions(-) diff --git a/tests/quicktests/run_pipeline_w_different_input_formats.ipynb b/tests/quicktests/run_pipeline_w_different_input_formats.ipynb index 1fab727..3d381d8 100644 --- a/tests/quicktests/run_pipeline_w_different_input_formats.ipynb +++ b/tests/quicktests/run_pipeline_w_different_input_formats.ipynb @@ -23,45 +23,48 @@ "metadata": {}, "outputs": [ { - "name": "stdout", + "name": "stderr", "output_type": "stream", "text": [ - "Starting directLFQ analysis.\n", - "using input type diann_precursors\n", - "Performing sample normalization.\n", - "to few values for normalization without missing values. Including missing values\n", - "Estimating lfq intensities.\n", - "46 prots total\n", - "using 10 processes\n", - "prot 0\n", - "Writing results files.\n", - "Analysis finished!\n", - "Starting directLFQ analysis.\n", - "using input type diann_peptide_based_on_precursor_ms1_and_ms2\n", - "Performing sample normalization.\n", - "Estimating lfq intensities.\n", - "840 prots total\n", - "using 10 processes\n", - "prot 0\n", - "prot 100\n", - "prot 200\n", - "prot 300\n", - "prot 400\n", - "prot 500\n", - "prot 600\n", - "prot 700\n", - "prot 800\n", - "Writing results files.\n", - "Analysis finished!\n", - "Starting directLFQ analysis.\n", - "using input type diann_precursor_ms1_and_ms2\n", - "Performing sample normalization.\n", - "Estimating lfq intensities.\n", - "46 prots total\n", - "using 10 processes\n", - "prot 0\n", - "Writing results files.\n", - "Analysis finished!\n" + "2024-01-16 18:30:46,103 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:30:46,236 - directlfq.utils - INFO - using input type diann_precursors\n", + "2024-01-16 18:30:46,305 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:30:46,306 - directlfq.normalization - INFO - to few values for normalization without missing values. Including missing values\n", + "2024-01-16 18:30:47,300 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:30:47,301 - directlfq.protein_intensity_estimation - INFO - 46 lfq-objects total\n", + "2024-01-16 18:30:47,315 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:30:47,373 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", + "2024-01-16 18:30:47,381 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:30:47,804 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:30:47,816 - directlfq.lfq_manager - INFO - Analysis finished!\n", + "2024-01-16 18:30:47,817 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:30:47,881 - directlfq.utils - INFO - using input type diann_peptide_based_on_precursor_ms1_and_ms2\n", + "2024-01-16 18:30:48,019 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:30:48,024 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:30:48,025 - directlfq.protein_intensity_estimation - INFO - 840 lfq-objects total\n", + "2024-01-16 18:30:48,297 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:30:48,351 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", + "2024-01-16 18:30:48,368 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:30:48,418 - directlfq.protein_intensity_estimation - INFO - lfq-object 100\n", + "2024-01-16 18:30:48,468 - directlfq.protein_intensity_estimation - INFO - lfq-object 200\n", + "2024-01-16 18:30:48,512 - directlfq.protein_intensity_estimation - INFO - lfq-object 300\n", + "2024-01-16 18:30:48,563 - directlfq.protein_intensity_estimation - INFO - lfq-object 400\n", + "2024-01-16 18:30:48,613 - directlfq.protein_intensity_estimation - INFO - lfq-object 500\n", + "2024-01-16 18:30:48,662 - directlfq.protein_intensity_estimation - INFO - lfq-object 600\n", + "2024-01-16 18:30:48,710 - directlfq.protein_intensity_estimation - INFO - lfq-object 700\n", + "2024-01-16 18:30:48,759 - directlfq.protein_intensity_estimation - INFO - lfq-object 800\n", + "2024-01-16 18:30:48,942 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:30:48,969 - directlfq.lfq_manager - INFO - Analysis finished!\n", + "2024-01-16 18:30:48,969 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:30:49,032 - directlfq.utils - INFO - using input type diann_precursor_ms1_and_ms2\n", + "2024-01-16 18:30:49,144 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:30:49,148 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:30:49,148 - directlfq.protein_intensity_estimation - INFO - 46 lfq-objects total\n", + "2024-01-16 18:30:49,163 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:30:49,217 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", + "2024-01-16 18:30:49,224 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:30:49,702 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:30:49,721 - directlfq.lfq_manager - INFO - Analysis finished!\n" ] } ], @@ -86,18 +89,19 @@ "metadata": {}, "outputs": [ { - "name": "stdout", + "name": "stderr", "output_type": "stream", "text": [ - "Starting directLFQ analysis.\n", - "using input type maxquant_peptides_leading_razor_protein\n", - "Performing sample normalization.\n", - "to few values for normalization without missing values. Including missing values\n", - "Estimating lfq intensities.\n", - "49 prots total\n", - "prot 0\n", - "Writing results files.\n", - "Analysis finished!\n" + "2024-01-16 18:30:49,727 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:30:49,912 - directlfq.utils - INFO - using input type maxquant_peptides_leading_razor_protein\n", + "2024-01-16 18:30:49,952 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:30:49,953 - directlfq.normalization - INFO - to few values for normalization without missing values. Including missing values\n", + "2024-01-16 18:30:49,958 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:30:49,959 - directlfq.protein_intensity_estimation - INFO - 49 lfq-objects total\n", + "2024-01-16 18:30:49,972 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:30:49,972 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:30:50,458 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:30:50,469 - directlfq.lfq_manager - INFO - Analysis finished!\n" ] } ], @@ -120,27 +124,30 @@ "metadata": {}, "outputs": [ { - "name": "stdout", + "name": "stderr", "output_type": "stream", "text": [ - "Starting directLFQ analysis.\n", - "using input type maxquant_evidence_leading_razor_protein\n", - "Performing sample normalization.\n", - "to few values for normalization without missing values. Including missing values\n", - "Estimating lfq intensities.\n", - "50 prots total\n", - "prot 0using 10 processes\n", - "\n", - "Writing results files.\n", - "Analysis finished!\n", - "Starting directLFQ analysis.\n", - "using input type maxquant_evidence_leading_razor_protein\n", - "Performing sample normalization.\n", - "Estimating lfq intensities.\n", - "50 prots total\n", - "prot 0\n", - "Writing results files.\n", - "Analysis finished!\n" + "2024-01-16 18:30:50,475 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:30:50,603 - directlfq.utils - INFO - using input type maxquant_evidence_leading_razor_protein\n", + "2024-01-16 18:30:50,701 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:30:50,702 - directlfq.normalization - INFO - to few values for normalization without missing values. Including missing values\n", + "2024-01-16 18:30:50,708 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:30:50,708 - directlfq.protein_intensity_estimation - INFO - 50 lfq-objects total\n", + "2024-01-16 18:30:50,723 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:30:50,781 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", + "2024-01-16 18:30:50,788 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:30:51,078 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:30:51,093 - directlfq.lfq_manager - INFO - Analysis finished!\n", + "2024-01-16 18:30:51,093 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:30:51,222 - directlfq.utils - INFO - using input type maxquant_evidence_leading_razor_protein\n", + "2024-01-16 18:30:51,324 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:30:51,325 - root - INFO - Normalizing only selected proteins\n", + "2024-01-16 18:30:51,331 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:30:51,331 - directlfq.protein_intensity_estimation - INFO - 50 lfq-objects total\n", + "2024-01-16 18:30:51,346 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:30:51,347 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:30:52,024 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:30:52,040 - directlfq.lfq_manager - INFO - Analysis finished!\n" ] } ], @@ -163,26 +170,29 @@ "metadata": {}, "outputs": [ { - "name": "stdout", + "name": "stderr", "output_type": "stream", "text": [ - "Starting directLFQ analysis.\n", - "using input type spectronaut_fragion_isotopes\n", - "Performing sample normalization.\n", - "Estimating lfq intensities.\n", - "50 prots total\n", - "prot 0\n", - "Writing results files.\n", - "Analysis finished!\n", - "Starting directLFQ analysis.\n", - "using input type spectronaut_fragion_isotopes\n", - "Performing sample normalization.\n", - "Estimating lfq intensities.\n", - "50 prots total\n", - "using 10 processes\n", - "prot 0\n", - "Writing results files.\n", - "Analysis finished!\n" + "2024-01-16 18:30:52,046 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:30:52,181 - directlfq.utils - INFO - using input type spectronaut_fragion_isotopes\n", + "2024-01-16 18:30:52,609 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:30:52,609 - root - INFO - Normalizing only selected proteins\n", + "2024-01-16 18:30:52,620 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:30:52,621 - directlfq.protein_intensity_estimation - INFO - 50 lfq-objects total\n", + "2024-01-16 18:30:52,639 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:30:52,639 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:30:53,978 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:30:54,005 - directlfq.lfq_manager - INFO - Analysis finished!\n", + "2024-01-16 18:30:54,005 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:30:54,132 - directlfq.utils - INFO - using input type spectronaut_fragion_isotopes\n", + "2024-01-16 18:30:54,580 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:30:54,588 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:30:54,589 - directlfq.protein_intensity_estimation - INFO - 50 lfq-objects total\n", + "2024-01-16 18:30:54,606 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:30:54,662 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", + "2024-01-16 18:30:54,669 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:30:55,131 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:30:55,159 - directlfq.lfq_manager - INFO - Analysis finished!\n" ] } ], @@ -193,9 +203,45 @@ "spectronaut_quicktest_file = f\"{quicktest_folder_spectronaut}/shortened_input.tsv\"\n", "spectronaut_protein_subset = f\"{quicktest_folder_spectronaut}/protein_subset.tsv\"\n", "if __name__ == '__main__': \n", - " lfq_manager.run_lfq(spectronaut_quicktest_file, selected_proteins_file=spectronaut_protein_subset, num_cores=1)\n", + " lfq_manager.run_lfq(spectronaut_quicktest_file, selected_proteins_file=spectronaut_protein_subset, num_cores=1, compile_normalized_ion_table=True)\n", " lfq_manager.run_lfq(spectronaut_quicktest_file)" ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([[1, 4],\n", + " [2, 5],\n", + " [3, 6]])" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "import pandas as pd\n", + "\n", + "# Sample dataframe\n", + "df = pd.DataFrame({'A': [1, 2, 3], 'B': [4, 5, 6]}, index=['x', 'y', 'z'])\n", + "\n", + "# Convert to NumPy array\n", + "array = df.to_numpy()\n", + "\n", + "display(array)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { @@ -214,7 +260,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.16" + "version": "3.8.17" }, "orig_nbformat": 4, "vscode": { diff --git a/tests/ratio_tests/compare_diapasef_diann.ipynb b/tests/ratio_tests/compare_diapasef_diann.ipynb index 110f3fc..8cd7e7d 100644 --- a/tests/ratio_tests/compare_diapasef_diann.ipynb +++ b/tests/ratio_tests/compare_diapasef_diann.ipynb @@ -80,590 +80,594 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-12-04 19:44:48,703 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", - "2023-12-04 19:44:48,775 - directlfq.utils - INFO - using input type diann_fragion_isotopes_topn\n", - "2023-12-04 19:45:15,091 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", - "2023-12-04 19:45:16,670 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", - "2023-12-04 19:45:16,716 - directlfq.protein_intensity_estimation - INFO - 11983 prots total\n", - "2023-12-04 19:45:16,810 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", - "2023-12-04 19:45:18,180 - directlfq.protein_intensity_estimation - INFO - prot 0\n", - "2023-12-04 19:45:18,287 - directlfq.protein_intensity_estimation - INFO - prot 300\n", - "2023-12-04 19:45:18,397 - directlfq.protein_intensity_estimation - INFO - prot 600\n", - "2023-12-04 19:45:18,626 - directlfq.protein_intensity_estimation - INFO - prot 900\n", - "2023-12-04 19:45:18,724 - directlfq.protein_intensity_estimation - INFO - prot 1200\n", - "2023-12-04 19:45:18,780 - directlfq.protein_intensity_estimation - INFO - prot 1500\n", - "2023-12-04 19:45:18,890 - directlfq.protein_intensity_estimation - INFO - prot 1800\n", - "2023-12-04 19:45:18,991 - directlfq.protein_intensity_estimation - INFO - prot 2100\n", - "2023-12-04 19:45:19,160 - directlfq.protein_intensity_estimation - INFO - prot 2400\n", - "2023-12-04 19:45:19,162 - directlfq.protein_intensity_estimation - INFO - prot 100\n", - "2023-12-04 19:45:19,311 - directlfq.protein_intensity_estimation - INFO - prot 2700\n", - "2023-12-04 19:45:19,744 - directlfq.protein_intensity_estimation - INFO - prot 700\n", - "2023-12-04 19:45:19,815 - directlfq.protein_intensity_estimation - INFO - prot 400\n", - "2023-12-04 19:45:19,854 - directlfq.protein_intensity_estimation - INFO - prot 200\n", - "2023-12-04 19:45:19,975 - directlfq.protein_intensity_estimation - INFO - prot 1000\n", - "2023-12-04 19:45:20,173 - directlfq.protein_intensity_estimation - INFO - prot 1300\n", - "2023-12-04 19:45:20,218 - directlfq.protein_intensity_estimation - INFO - prot 1600\n", - "2023-12-04 19:45:20,508 - directlfq.protein_intensity_estimation - INFO - prot 1900\n", - "2023-12-04 19:45:20,567 - directlfq.protein_intensity_estimation - INFO - prot 3000\n", - "2023-12-04 19:45:20,614 - directlfq.protein_intensity_estimation - INFO - prot 2500\n", - "2023-12-04 19:45:20,693 - directlfq.protein_intensity_estimation - INFO - prot 2200\n", - "2023-12-04 19:45:20,795 - directlfq.protein_intensity_estimation - INFO - prot 2800\n", - "2023-12-04 19:45:21,124 - directlfq.protein_intensity_estimation - INFO - prot 500\n", - "2023-12-04 19:45:21,158 - directlfq.protein_intensity_estimation - INFO - prot 800\n", - "2023-12-04 19:45:21,260 - directlfq.protein_intensity_estimation - INFO - prot 1100\n", - "2023-12-04 19:45:21,277 - directlfq.protein_intensity_estimation - INFO - prot 1400\n", + "2024-01-16 18:15:46,365 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:15:46,438 - directlfq.utils - INFO - using input type diann_fragion_isotopes_topn\n", + "2024-01-16 18:16:12,575 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:16:14,094 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:16:14,139 - directlfq.protein_intensity_estimation - INFO - 11983 lfq-objects total\n", + "2024-01-16 18:16:17,480 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:16:17,565 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", + "2024-01-16 18:16:17,755 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:16:17,927 - directlfq.protein_intensity_estimation - INFO - lfq-object 300\n", + "2024-01-16 18:16:18,105 - directlfq.protein_intensity_estimation - INFO - lfq-object 600\n", + "2024-01-16 18:16:18,385 - directlfq.protein_intensity_estimation - INFO - lfq-object 900\n", + "2024-01-16 18:16:18,541 - directlfq.protein_intensity_estimation - INFO - lfq-object 1200\n", + "2024-01-16 18:16:18,614 - directlfq.protein_intensity_estimation - INFO - lfq-object 1500\n", + "2024-01-16 18:16:19,000 - directlfq.protein_intensity_estimation - INFO - lfq-object 1800\n", + "2024-01-16 18:16:19,175 - directlfq.protein_intensity_estimation - INFO - lfq-object 2100\n", + "2024-01-16 18:16:19,369 - directlfq.protein_intensity_estimation - INFO - lfq-object 100\n", + "2024-01-16 18:16:19,433 - directlfq.protein_intensity_estimation - INFO - lfq-object 2400\n", + "2024-01-16 18:16:19,694 - directlfq.protein_intensity_estimation - INFO - lfq-object 2700\n", + "2024-01-16 18:16:20,337 - directlfq.protein_intensity_estimation - INFO - lfq-object 700\n", + "2024-01-16 18:16:20,347 - directlfq.protein_intensity_estimation - INFO - lfq-object 400\n", + "2024-01-16 18:16:20,678 - directlfq.protein_intensity_estimation - INFO - lfq-object 200\n", + "2024-01-16 18:16:20,743 - directlfq.protein_intensity_estimation - INFO - lfq-object 1000\n", + "2024-01-16 18:16:20,950 - directlfq.protein_intensity_estimation - INFO - lfq-object 1600\n", + "2024-01-16 18:16:20,967 - directlfq.protein_intensity_estimation - INFO - lfq-object 1300\n", + "2024-01-16 18:16:21,522 - directlfq.protein_intensity_estimation - INFO - lfq-object 1900\n", + "2024-01-16 18:16:21,745 - directlfq.protein_intensity_estimation - INFO - lfq-object 2200\n", + "2024-01-16 18:16:21,841 - directlfq.protein_intensity_estimation - INFO - lfq-object 2500\n", + "2024-01-16 18:16:21,994 - directlfq.protein_intensity_estimation - INFO - lfq-object 3000\n", + "2024-01-16 18:16:22,269 - directlfq.protein_intensity_estimation - INFO - lfq-object 2800\n", + "2024-01-16 18:16:22,638 - directlfq.protein_intensity_estimation - INFO - lfq-object 500\n", + "2024-01-16 18:16:22,893 - directlfq.protein_intensity_estimation - INFO - lfq-object 800\n", + "2024-01-16 18:16:22,939 - directlfq.protein_intensity_estimation - INFO - lfq-object 1100\n", + "2024-01-16 18:16:22,965 - directlfq.protein_intensity_estimation - INFO - lfq-object 1400\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:45:21,500 - directlfq.protein_intensity_estimation - INFO - prot 2600\n", + "2024-01-16 18:16:23,467 - directlfq.protein_intensity_estimation - INFO - lfq-object 2600\n", + "2024-01-16 18:16:23,473 - directlfq.protein_intensity_estimation - INFO - lfq-object 1700\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:45:21,587 - directlfq.protein_intensity_estimation - INFO - prot 3100\n", - "2023-12-04 19:45:21,678 - directlfq.protein_intensity_estimation - INFO - prot 1700\n", - "2023-12-04 19:45:21,808 - directlfq.protein_intensity_estimation - INFO - prot 2300\n", - "2023-12-04 19:45:21,856 - directlfq.protein_intensity_estimation - INFO - prot 2000\n", - "2023-12-04 19:45:22,038 - directlfq.protein_intensity_estimation - INFO - prot 2900\n", - "2023-12-04 19:45:22,653 - directlfq.protein_intensity_estimation - INFO - prot 3300\n", - "2023-12-04 19:45:22,848 - directlfq.protein_intensity_estimation - INFO - prot 3600\n", - "2023-12-04 19:45:22,858 - directlfq.protein_intensity_estimation - INFO - prot 3200\n", - "2023-12-04 19:45:22,975 - directlfq.protein_intensity_estimation - INFO - prot 3900\n", - "2023-12-04 19:45:23,102 - directlfq.protein_intensity_estimation - INFO - prot 4200\n", - "2023-12-04 19:45:23,291 - directlfq.protein_intensity_estimation - INFO - prot 4500\n", - "2023-12-04 19:45:23,396 - directlfq.protein_intensity_estimation - INFO - prot 4800\n", - "2023-12-04 19:45:23,535 - directlfq.protein_intensity_estimation - INFO - prot 5100\n", - "2023-12-04 19:45:23,590 - directlfq.protein_intensity_estimation - INFO - prot 3400\n", - "2023-12-04 19:45:23,640 - directlfq.protein_intensity_estimation - INFO - prot 3700\n", - "2023-12-04 19:45:23,680 - directlfq.protein_intensity_estimation - INFO - prot 5400\n", - "2023-12-04 19:45:23,902 - directlfq.protein_intensity_estimation - INFO - prot 4300\n", - "2023-12-04 19:45:23,919 - directlfq.protein_intensity_estimation - INFO - prot 5700\n", - "2023-12-04 19:45:23,976 - directlfq.protein_intensity_estimation - INFO - prot 4000\n", - "2023-12-04 19:45:24,087 - directlfq.protein_intensity_estimation - INFO - prot 6000\n", - "2023-12-04 19:45:24,106 - directlfq.protein_intensity_estimation - INFO - prot 4900\n", - "2023-12-04 19:45:24,425 - directlfq.protein_intensity_estimation - INFO - prot 3500\n", - "2023-12-04 19:45:24,478 - directlfq.protein_intensity_estimation - INFO - prot 4600\n", - "2023-12-04 19:45:24,573 - directlfq.protein_intensity_estimation - INFO - prot 3800\n", - "2023-12-04 19:45:24,700 - directlfq.protein_intensity_estimation - INFO - prot 5500\n", - "2023-12-04 19:45:24,774 - directlfq.protein_intensity_estimation - INFO - prot 5200\n", - "2023-12-04 19:45:24,809 - directlfq.protein_intensity_estimation - INFO - prot 5800\n", - "2023-12-04 19:45:25,213 - directlfq.protein_intensity_estimation - INFO - prot 4700\n", - "2023-12-04 19:45:25,215 - directlfq.protein_intensity_estimation - INFO - prot 4100\n", - "2023-12-04 19:45:25,251 - directlfq.protein_intensity_estimation - INFO - prot 6100\n", - "2023-12-04 19:45:25,421 - directlfq.protein_intensity_estimation - INFO - prot 5000\n", - "2023-12-04 19:45:25,471 - directlfq.protein_intensity_estimation - INFO - prot 5600\n", - "2023-12-04 19:45:25,434 - directlfq.protein_intensity_estimation - INFO - prot 6300\n", - "2023-12-04 19:45:25,438 - directlfq.protein_intensity_estimation - INFO - prot 4400\n", - "2023-12-04 19:45:25,566 - directlfq.protein_intensity_estimation - INFO - prot 5900\n", - "2023-12-04 19:45:25,853 - directlfq.protein_intensity_estimation - INFO - prot 5300\n", - "2023-12-04 19:45:25,867 - directlfq.protein_intensity_estimation - INFO - prot 6600\n", - "2023-12-04 19:45:26,008 - directlfq.protein_intensity_estimation - INFO - prot 6200\n", - "2023-12-04 19:45:26,203 - directlfq.protein_intensity_estimation - INFO - prot 6900\n", - "2023-12-04 19:45:26,523 - directlfq.protein_intensity_estimation - INFO - prot 7200\n", - "2023-12-04 19:45:26,686 - directlfq.protein_intensity_estimation - INFO - prot 7500\n", - "2023-12-04 19:45:26,884 - directlfq.protein_intensity_estimation - INFO - prot 7800\n", - "2023-12-04 19:45:26,990 - directlfq.protein_intensity_estimation - INFO - prot 6400\n", - "2023-12-04 19:45:27,025 - directlfq.protein_intensity_estimation - INFO - prot 8100\n", - "2023-12-04 19:45:27,201 - directlfq.protein_intensity_estimation - INFO - prot 8400\n", - "2023-12-04 19:45:27,343 - directlfq.protein_intensity_estimation - INFO - prot 7000\n", - "2023-12-04 19:45:27,382 - directlfq.protein_intensity_estimation - INFO - prot 8700\n", - "2023-12-04 19:45:27,424 - directlfq.protein_intensity_estimation - INFO - prot 6700\n", - "2023-12-04 19:45:27,520 - directlfq.protein_intensity_estimation - INFO - prot 9000\n", - "2023-12-04 19:45:27,717 - directlfq.protein_intensity_estimation - INFO - prot 7300\n", - "2023-12-04 19:45:27,954 - directlfq.protein_intensity_estimation - INFO - prot 7600\n", - "2023-12-04 19:45:28,174 - directlfq.protein_intensity_estimation - INFO - prot 8500\n", - "2023-12-04 19:45:28,229 - directlfq.protein_intensity_estimation - INFO - prot 7900\n", - "2023-12-04 19:45:28,453 - directlfq.protein_intensity_estimation - INFO - prot 7100\n", - "2023-12-04 19:45:28,583 - directlfq.protein_intensity_estimation - INFO - prot 8200\n", - "2023-12-04 19:45:28,710 - directlfq.protein_intensity_estimation - INFO - prot 8800\n", - "2023-12-04 19:45:28,718 - directlfq.protein_intensity_estimation - INFO - prot 6500\n", - "2023-12-04 19:45:29,072 - directlfq.protein_intensity_estimation - INFO - prot 9100\n", - "2023-12-04 19:45:29,102 - directlfq.protein_intensity_estimation - INFO - prot 7700\n", - "2023-12-04 19:45:29,219 - directlfq.protein_intensity_estimation - INFO - prot 6800\n", - "2023-12-04 19:45:29,227 - directlfq.protein_intensity_estimation - INFO - prot 7400\n", - "2023-12-04 19:45:29,395 - directlfq.protein_intensity_estimation - INFO - prot 8600\n", - "2023-12-04 19:45:29,548 - directlfq.protein_intensity_estimation - INFO - prot 9300\n", - "2023-12-04 19:45:29,581 - directlfq.protein_intensity_estimation - INFO - prot 8000\n", - "2023-12-04 19:45:29,829 - directlfq.protein_intensity_estimation - INFO - prot 8300\n", - "2023-12-04 19:45:29,921 - directlfq.protein_intensity_estimation - INFO - prot 8900\n", - "2023-12-04 19:45:30,150 - directlfq.protein_intensity_estimation - INFO - prot 9200\n", - "2023-12-04 19:45:30,253 - directlfq.protein_intensity_estimation - INFO - prot 9600\n", - "2023-12-04 19:45:30,606 - directlfq.protein_intensity_estimation - INFO - prot 9900\n", - "2023-12-04 19:45:30,631 - directlfq.protein_intensity_estimation - INFO - prot 9400\n", - "2023-12-04 19:45:30,781 - directlfq.protein_intensity_estimation - INFO - prot 10200\n", - "2023-12-04 19:45:30,970 - directlfq.protein_intensity_estimation - INFO - prot 10500\n", - "2023-12-04 19:45:31,090 - directlfq.protein_intensity_estimation - INFO - prot 10800\n", - "2023-12-04 19:45:31,335 - directlfq.protein_intensity_estimation - INFO - prot 11100\n", - "2023-12-04 19:45:31,456 - directlfq.protein_intensity_estimation - INFO - prot 9700\n", - "2023-12-04 19:45:31,506 - directlfq.protein_intensity_estimation - INFO - prot 10000\n", - "2023-12-04 19:45:31,466 - directlfq.protein_intensity_estimation - INFO - prot 11400\n", - "2023-12-04 19:45:31,652 - directlfq.protein_intensity_estimation - INFO - prot 11700\n", - "2023-12-04 19:45:31,653 - directlfq.protein_intensity_estimation - INFO - prot 9500\n", - "2023-12-04 19:45:31,803 - directlfq.protein_intensity_estimation - INFO - prot 10300\n", - "2023-12-04 19:45:31,998 - directlfq.protein_intensity_estimation - INFO - prot 10600\n", - "2023-12-04 19:45:32,324 - directlfq.protein_intensity_estimation - INFO - prot 10900\n", - "2023-12-04 19:45:32,435 - directlfq.protein_intensity_estimation - INFO - prot 11200\n", - "2023-12-04 19:45:32,613 - directlfq.protein_intensity_estimation - INFO - prot 9800\n", - "2023-12-04 19:45:32,641 - directlfq.protein_intensity_estimation - INFO - prot 10100\n", - "2023-12-04 19:45:32,684 - directlfq.protein_intensity_estimation - INFO - prot 11500\n", - "2023-12-04 19:45:32,866 - directlfq.protein_intensity_estimation - INFO - prot 11800\n", - "2023-12-04 19:45:32,969 - directlfq.protein_intensity_estimation - INFO - prot 10400\n", - "2023-12-04 19:45:32,991 - directlfq.protein_intensity_estimation - INFO - prot 10700\n", - "2023-12-04 19:45:33,318 - directlfq.protein_intensity_estimation - INFO - prot 11000\n", - "2023-12-04 19:45:33,559 - directlfq.protein_intensity_estimation - INFO - prot 11300\n", - "2023-12-04 19:45:33,935 - directlfq.protein_intensity_estimation - INFO - prot 11600\n", - "2023-12-04 19:45:33,972 - directlfq.protein_intensity_estimation - INFO - prot 11900\n", - "2023-12-04 19:45:49,696 - directlfq.lfq_manager - INFO - Writing results files.\n", - "2023-12-04 19:45:54,630 - directlfq.lfq_manager - INFO - Analysis finished!\n", - "2023-12-04 19:45:54,694 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", - "2023-12-04 19:45:54,757 - directlfq.utils - INFO - using input type diann_precursor_ms1_and_ms2\n", - "2023-12-04 19:46:08,841 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", - "2023-12-04 19:46:09,143 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", - "2023-12-04 19:46:09,166 - directlfq.protein_intensity_estimation - INFO - 11983 prots total\n", - "2023-12-04 19:46:09,249 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", - "2023-12-04 19:46:10,552 - directlfq.protein_intensity_estimation - INFO - prot 0\n", - "2023-12-04 19:46:10,633 - directlfq.protein_intensity_estimation - INFO - prot 300\n", - "2023-12-04 19:46:10,715 - directlfq.protein_intensity_estimation - INFO - prot 600\n", - "2023-12-04 19:46:10,914 - directlfq.protein_intensity_estimation - INFO - prot 900\n", - "2023-12-04 19:46:10,947 - directlfq.protein_intensity_estimation - INFO - prot 1200\n", - "2023-12-04 19:46:11,027 - directlfq.protein_intensity_estimation - INFO - prot 1500\n", - "2023-12-04 19:46:11,107 - directlfq.protein_intensity_estimation - INFO - prot 1800\n", - "2023-12-04 19:46:11,188 - directlfq.protein_intensity_estimation - INFO - prot 2100\n", - "2023-12-04 19:46:11,212 - directlfq.protein_intensity_estimation - INFO - prot 100\n", - "2023-12-04 19:46:11,342 - directlfq.protein_intensity_estimation - INFO - prot 2400\n", - "2023-12-04 19:46:11,463 - directlfq.protein_intensity_estimation - INFO - prot 2700\n", - "2023-12-04 19:46:11,601 - directlfq.protein_intensity_estimation - INFO - prot 700\n", - "2023-12-04 19:46:11,654 - directlfq.protein_intensity_estimation - INFO - prot 400\n", - "2023-12-04 19:46:11,672 - directlfq.protein_intensity_estimation - INFO - prot 200\n", - "2023-12-04 19:46:11,833 - directlfq.protein_intensity_estimation - INFO - prot 1000\n", - "2023-12-04 19:46:11,992 - directlfq.protein_intensity_estimation - INFO - prot 1300\n", - "2023-12-04 19:46:12,008 - directlfq.protein_intensity_estimation - INFO - prot 1600\n", - "2023-12-04 19:46:12,127 - directlfq.protein_intensity_estimation - INFO - prot 3000\n", - "2023-12-04 19:46:12,252 - directlfq.protein_intensity_estimation - INFO - prot 1900\n", - "2023-12-04 19:46:12,318 - directlfq.protein_intensity_estimation - INFO - prot 2200\n", - "2023-12-04 19:46:12,327 - directlfq.protein_intensity_estimation - INFO - prot 2500\n", - "2023-12-04 19:46:12,480 - directlfq.protein_intensity_estimation - INFO - prot 2800\n", - "2023-12-04 19:46:12,586 - directlfq.protein_intensity_estimation - INFO - prot 500\n", - "2023-12-04 19:46:12,712 - directlfq.protein_intensity_estimation - INFO - prot 3100\n", - "2023-12-04 19:46:12,719 - directlfq.protein_intensity_estimation - INFO - prot 800\n", - "2023-12-04 19:46:12,740 - directlfq.protein_intensity_estimation - INFO - prot 1100\n", - "2023-12-04 19:46:12,834 - directlfq.protein_intensity_estimation - INFO - prot 1400\n", - "2023-12-04 19:46:12,973 - directlfq.protein_intensity_estimation - INFO - prot 2600\n", - "2023-12-04 19:46:13,010 - directlfq.protein_intensity_estimation - INFO - prot 1700\n", - "2023-12-04 19:46:13,115 - directlfq.protein_intensity_estimation - INFO - prot 2300\n", - "2023-12-04 19:46:13,203 - directlfq.protein_intensity_estimation - INFO - prot 2000\n", - "2023-12-04 19:46:13,427 - directlfq.protein_intensity_estimation - INFO - prot 2900\n", - "2023-12-04 19:46:13,561 - directlfq.protein_intensity_estimation - INFO - prot 3200\n", - "2023-12-04 19:46:13,637 - directlfq.protein_intensity_estimation - INFO - prot 3300\n", - "2023-12-04 19:46:13,764 - directlfq.protein_intensity_estimation - INFO - prot 3600\n", - "2023-12-04 19:46:13,898 - directlfq.protein_intensity_estimation - INFO - prot 3900\n", - "2023-12-04 19:46:14,009 - directlfq.protein_intensity_estimation - INFO - prot 4200\n", - "2023-12-04 19:46:14,184 - directlfq.protein_intensity_estimation - INFO - prot 4500\n", - "2023-12-04 19:46:14,201 - directlfq.protein_intensity_estimation - INFO - prot 3400\n", - "2023-12-04 19:46:14,206 - directlfq.protein_intensity_estimation - INFO - prot 3700\n", - "2023-12-04 19:46:14,283 - directlfq.protein_intensity_estimation - INFO - prot 4800\n", - "2023-12-04 19:46:14,380 - directlfq.protein_intensity_estimation - INFO - prot 5100\n", - "2023-12-04 19:46:14,467 - directlfq.protein_intensity_estimation - INFO - prot 5400\n", - "2023-12-04 19:46:14,506 - directlfq.protein_intensity_estimation - INFO - prot 4000\n", - "2023-12-04 19:46:14,492 - directlfq.protein_intensity_estimation - INFO - prot 4300\n", - "2023-12-04 19:46:14,615 - directlfq.protein_intensity_estimation - INFO - prot 5700\n", - "2023-12-04 19:46:14,617 - directlfq.protein_intensity_estimation - INFO - prot 3500\n", - "2023-12-04 19:46:14,632 - directlfq.protein_intensity_estimation - INFO - prot 3800\n", - "2023-12-04 19:46:14,719 - directlfq.protein_intensity_estimation - INFO - prot 6000\n", - "2023-12-04 19:46:14,771 - directlfq.protein_intensity_estimation - INFO - prot 4900\n", - "2023-12-04 19:46:14,944 - directlfq.protein_intensity_estimation - INFO - prot 4600\n", - "2023-12-04 19:46:15,073 - directlfq.protein_intensity_estimation - INFO - prot 5500\n", - "2023-12-04 19:46:15,124 - directlfq.protein_intensity_estimation - INFO - prot 5800\n", - "2023-12-04 19:46:15,136 - directlfq.protein_intensity_estimation - INFO - prot 5200\n", - "2023-12-04 19:46:15,227 - directlfq.protein_intensity_estimation - INFO - prot 6300\n", - "2023-12-04 19:46:15,258 - directlfq.protein_intensity_estimation - INFO - prot 6100\n", - "2023-12-04 19:46:15,274 - directlfq.protein_intensity_estimation - INFO - prot 4100\n", - "2023-12-04 19:46:15,341 - directlfq.protein_intensity_estimation - INFO - prot 4700\n", - "2023-12-04 19:46:15,418 - directlfq.protein_intensity_estimation - INFO - prot 6600\n", - "2023-12-04 19:46:15,467 - directlfq.protein_intensity_estimation - INFO - prot 5600\n", - "2023-12-04 19:46:15,476 - directlfq.protein_intensity_estimation - INFO - prot 5000\n", - "2023-12-04 19:46:15,534 - directlfq.protein_intensity_estimation - INFO - prot 5900\n", - "2023-12-04 19:46:15,536 - directlfq.protein_intensity_estimation - INFO - prot 4400\n", - "2023-12-04 19:46:15,771 - directlfq.protein_intensity_estimation - INFO - prot 6200\n", - "2023-12-04 19:46:15,817 - directlfq.protein_intensity_estimation - INFO - prot 5300\n", - "2023-12-04 19:46:16,166 - directlfq.protein_intensity_estimation - INFO - prot 6900\n", - "2023-12-04 19:46:16,279 - directlfq.protein_intensity_estimation - INFO - prot 6400\n", - "2023-12-04 19:46:16,348 - directlfq.protein_intensity_estimation - INFO - prot 7200\n", - "2023-12-04 19:46:16,449 - directlfq.protein_intensity_estimation - INFO - prot 7500\n", - "2023-12-04 19:46:16,548 - directlfq.protein_intensity_estimation - INFO - prot 6700\n", - "2023-12-04 19:46:16,557 - directlfq.protein_intensity_estimation - INFO - prot 7800\n", - "2023-12-04 19:46:16,654 - directlfq.protein_intensity_estimation - INFO - prot 8100\n", - "2023-12-04 19:46:16,740 - directlfq.protein_intensity_estimation - INFO - prot 8400\n", - "2023-12-04 19:46:16,846 - directlfq.protein_intensity_estimation - INFO - prot 7000\n", - "2023-12-04 19:46:16,915 - directlfq.protein_intensity_estimation - INFO - prot 8700\n", - "2023-12-04 19:46:17,044 - directlfq.protein_intensity_estimation - INFO - prot 9000\n", - "2023-12-04 19:46:17,060 - directlfq.protein_intensity_estimation - INFO - prot 7300\n", - "2023-12-04 19:46:17,075 - directlfq.protein_intensity_estimation - INFO - prot 7600\n", - "2023-12-04 19:46:17,120 - directlfq.protein_intensity_estimation - INFO - prot 6500\n", - "2023-12-04 19:46:17,311 - directlfq.protein_intensity_estimation - INFO - prot 8500\n", - "2023-12-04 19:46:17,393 - directlfq.protein_intensity_estimation - INFO - prot 7100\n", - "2023-12-04 19:46:17,395 - directlfq.protein_intensity_estimation - INFO - prot 7900\n", - "2023-12-04 19:46:17,454 - directlfq.protein_intensity_estimation - INFO - prot 8200\n", - "2023-12-04 19:46:17,479 - directlfq.protein_intensity_estimation - INFO - prot 6800\n", - "2023-12-04 19:46:17,679 - directlfq.protein_intensity_estimation - INFO - prot 8800\n", - "2023-12-04 19:46:17,782 - directlfq.protein_intensity_estimation - INFO - prot 7700\n", - "2023-12-04 19:46:17,815 - directlfq.protein_intensity_estimation - INFO - prot 9100\n", - "2023-12-04 19:46:17,876 - directlfq.protein_intensity_estimation - INFO - prot 7400\n", - "2023-12-04 19:46:17,986 - directlfq.protein_intensity_estimation - INFO - prot 8600\n", - "2023-12-04 19:46:18,118 - directlfq.protein_intensity_estimation - INFO - prot 9300\n", - "2023-12-04 19:46:18,153 - directlfq.protein_intensity_estimation - INFO - prot 8000\n", - "2023-12-04 19:46:18,222 - directlfq.protein_intensity_estimation - INFO - prot 8300\n", - "2023-12-04 19:46:18,390 - directlfq.protein_intensity_estimation - INFO - prot 9600\n", - "2023-12-04 19:46:18,415 - directlfq.protein_intensity_estimation - INFO - prot 8900\n", - "2023-12-04 19:46:18,466 - directlfq.protein_intensity_estimation - INFO - prot 9200\n", - "2023-12-04 19:46:18,545 - directlfq.protein_intensity_estimation - INFO - prot 9900\n", - "2023-12-04 19:46:18,709 - directlfq.protein_intensity_estimation - INFO - prot 10200\n", - "2023-12-04 19:46:18,779 - directlfq.protein_intensity_estimation - INFO - prot 9400\n", - "2023-12-04 19:46:18,834 - directlfq.protein_intensity_estimation - INFO - prot 10500\n", - "2023-12-04 19:46:19,073 - directlfq.protein_intensity_estimation - INFO - prot 10800\n", - "2023-12-04 19:46:19,140 - directlfq.protein_intensity_estimation - INFO - prot 10000\n", - "2023-12-04 19:46:19,151 - directlfq.protein_intensity_estimation - INFO - prot 9700\n", - "2023-12-04 19:46:19,219 - directlfq.protein_intensity_estimation - INFO - prot 11100\n", - "2023-12-04 19:46:19,319 - directlfq.protein_intensity_estimation - INFO - prot 10300\n", - "2023-12-04 19:46:19,357 - directlfq.protein_intensity_estimation - INFO - prot 11400\n", - "2023-12-04 19:46:19,484 - directlfq.protein_intensity_estimation - INFO - prot 10600\n", - "2023-12-04 19:46:19,495 - directlfq.protein_intensity_estimation - INFO - prot 11700\n", - "2023-12-04 19:46:19,511 - directlfq.protein_intensity_estimation - INFO - prot 9500\n", - "2023-12-04 19:46:19,773 - directlfq.protein_intensity_estimation - INFO - prot 10100\n", - "2023-12-04 19:46:19,791 - directlfq.protein_intensity_estimation - INFO - prot 10900\n", - "2023-12-04 19:46:19,882 - directlfq.protein_intensity_estimation - INFO - prot 9800\n", - "2023-12-04 19:46:19,946 - directlfq.protein_intensity_estimation - INFO - prot 11200\n", - "2023-12-04 19:46:20,070 - directlfq.protein_intensity_estimation - INFO - prot 11500\n", - "2023-12-04 19:46:20,109 - directlfq.protein_intensity_estimation - INFO - prot 10700\n", - "2023-12-04 19:46:20,119 - directlfq.protein_intensity_estimation - INFO - prot 10400\n", - "2023-12-04 19:46:20,228 - directlfq.protein_intensity_estimation - INFO - prot 11800\n", - "2023-12-04 19:46:20,406 - directlfq.protein_intensity_estimation - INFO - prot 11000\n", - "2023-12-04 19:46:20,733 - directlfq.protein_intensity_estimation - INFO - prot 11300\n", - "2023-12-04 19:46:20,861 - directlfq.protein_intensity_estimation - INFO - prot 11600\n", - "2023-12-04 19:46:20,966 - directlfq.protein_intensity_estimation - INFO - prot 11900\n", - "2023-12-04 19:46:35,575 - directlfq.lfq_manager - INFO - Writing results files.\n", - "2023-12-04 19:46:38,341 - directlfq.lfq_manager - INFO - Analysis finished!\n", - "2023-12-04 19:46:38,390 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", - "2023-12-04 19:46:38,490 - directlfq.utils - INFO - using input type diann_precursors\n", - "2023-12-04 19:46:44,068 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", - "2023-12-04 19:46:44,230 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", - "2023-12-04 19:46:44,242 - directlfq.protein_intensity_estimation - INFO - 11983 prots total\n", - "2023-12-04 19:46:44,314 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", - "2023-12-04 19:46:45,603 - directlfq.protein_intensity_estimation - INFO - prot 0\n", - "2023-12-04 19:46:45,670 - directlfq.protein_intensity_estimation - INFO - prot 300\n", - "2023-12-04 19:46:45,738 - directlfq.protein_intensity_estimation - INFO - prot 600\n", - "2023-12-04 19:46:45,805 - directlfq.protein_intensity_estimation - INFO - prot 900\n", - "2023-12-04 19:46:45,869 - directlfq.protein_intensity_estimation - INFO - prot 1200\n", - "2023-12-04 19:46:45,934 - directlfq.protein_intensity_estimation - INFO - prot 1500\n", - "2023-12-04 19:46:46,003 - directlfq.protein_intensity_estimation - INFO - prot 1800\n", - "2023-12-04 19:46:46,076 - directlfq.protein_intensity_estimation - INFO - prot 100\n", - "2023-12-04 19:46:46,077 - directlfq.protein_intensity_estimation - INFO - prot 2100\n", - "2023-12-04 19:46:46,192 - directlfq.protein_intensity_estimation - INFO - prot 2400\n", - "2023-12-04 19:46:46,229 - directlfq.protein_intensity_estimation - INFO - prot 700\n", - "2023-12-04 19:46:46,240 - directlfq.protein_intensity_estimation - INFO - prot 400\n", - "2023-12-04 19:46:46,245 - directlfq.protein_intensity_estimation - INFO - prot 200\n", - "2023-12-04 19:46:46,307 - directlfq.protein_intensity_estimation - INFO - prot 2700\n", - "2023-12-04 19:46:46,427 - directlfq.protein_intensity_estimation - INFO - prot 1300\n", - "2023-12-04 19:46:46,489 - directlfq.protein_intensity_estimation - INFO - prot 1000\n", - "2023-12-04 19:46:46,565 - directlfq.protein_intensity_estimation - INFO - prot 1600\n", - "2023-12-04 19:46:46,642 - directlfq.protein_intensity_estimation - INFO - prot 1900\n", - "2023-12-04 19:46:46,678 - directlfq.protein_intensity_estimation - INFO - prot 3000\n", - "2023-12-04 19:46:46,695 - directlfq.protein_intensity_estimation - INFO - prot 500\n", - "2023-12-04 19:46:46,717 - directlfq.protein_intensity_estimation - INFO - prot 2200\n", - "2023-12-04 19:46:46,750 - directlfq.protein_intensity_estimation - INFO - prot 2500\n", - "2023-12-04 19:46:46,822 - directlfq.protein_intensity_estimation - INFO - prot 1400\n", - "2023-12-04 19:46:46,833 - directlfq.protein_intensity_estimation - INFO - prot 800\n", - "2023-12-04 19:46:46,960 - directlfq.protein_intensity_estimation - INFO - prot 2800\n", - "2023-12-04 19:46:46,963 - directlfq.protein_intensity_estimation - INFO - prot 1100\n", - "2023-12-04 19:46:46,969 - directlfq.protein_intensity_estimation - INFO - prot 2600\n", - "2023-12-04 19:46:47,044 - directlfq.protein_intensity_estimation - INFO - prot 3100\n", - "2023-12-04 19:46:47,122 - directlfq.protein_intensity_estimation - INFO - prot 2300\n", - "2023-12-04 19:46:47,175 - directlfq.protein_intensity_estimation - INFO - prot 2000\n", - "2023-12-04 19:46:47,267 - directlfq.protein_intensity_estimation - INFO - prot 1700\n", - "2023-12-04 19:46:47,396 - directlfq.protein_intensity_estimation - INFO - prot 3300\n", - "2023-12-04 19:46:47,513 - directlfq.protein_intensity_estimation - INFO - prot 2900\n", - "2023-12-04 19:46:47,576 - directlfq.protein_intensity_estimation - INFO - prot 3200\n", - "2023-12-04 19:46:47,646 - directlfq.protein_intensity_estimation - INFO - prot 3600\n", - "2023-12-04 19:46:47,750 - directlfq.protein_intensity_estimation - INFO - prot 3900\n", - "2023-12-04 19:46:47,798 - directlfq.protein_intensity_estimation - INFO - prot 3400\n", - "2023-12-04 19:46:47,825 - directlfq.protein_intensity_estimation - INFO - prot 4200\n", - "2023-12-04 19:46:47,857 - directlfq.protein_intensity_estimation - INFO - prot 4500\n", - "2023-12-04 19:46:47,893 - directlfq.protein_intensity_estimation - INFO - prot 3700\n", - "2023-12-04 19:46:48,008 - directlfq.protein_intensity_estimation - INFO - prot 3500\n", - "2023-12-04 19:46:48,023 - directlfq.protein_intensity_estimation - INFO - prot 4800\n", - "2023-12-04 19:46:48,088 - directlfq.protein_intensity_estimation - INFO - prot 4300\n", - "2023-12-04 19:46:48,091 - directlfq.protein_intensity_estimation - INFO - prot 4000\n", - "2023-12-04 19:46:48,121 - directlfq.protein_intensity_estimation - INFO - prot 3800\n", - "2023-12-04 19:46:48,183 - directlfq.protein_intensity_estimation - INFO - prot 5100\n", - "2023-12-04 19:46:48,233 - directlfq.protein_intensity_estimation - INFO - prot 4900\n", - "2023-12-04 19:46:48,255 - directlfq.protein_intensity_estimation - INFO - prot 5400\n", - "2023-12-04 19:46:48,299 - directlfq.protein_intensity_estimation - INFO - prot 5700\n", - "2023-12-04 19:46:48,317 - directlfq.protein_intensity_estimation - INFO - prot 4600\n", - "2023-12-04 19:46:48,489 - directlfq.protein_intensity_estimation - INFO - prot 4100\n", - "2023-12-04 19:46:48,493 - directlfq.protein_intensity_estimation - INFO - prot 6000\n", - "2023-12-04 19:46:48,505 - directlfq.protein_intensity_estimation - INFO - prot 4700\n", - "2023-12-04 19:46:48,530 - directlfq.protein_intensity_estimation - INFO - prot 5800\n", - "2023-12-04 19:46:48,536 - directlfq.protein_intensity_estimation - INFO - prot 5500\n", - "2023-12-04 19:46:48,555 - directlfq.protein_intensity_estimation - INFO - prot 6300\n", - "2023-12-04 19:46:48,577 - directlfq.protein_intensity_estimation - INFO - prot 5200\n", - "2023-12-04 19:46:48,589 - directlfq.protein_intensity_estimation - INFO - prot 4400\n", - "2023-12-04 19:46:48,617 - directlfq.protein_intensity_estimation - INFO - prot 5000\n", - "2023-12-04 19:46:48,715 - directlfq.protein_intensity_estimation - INFO - prot 6600\n", - "2023-12-04 19:46:48,748 - directlfq.protein_intensity_estimation - INFO - prot 5900\n", - "2023-12-04 19:46:48,791 - directlfq.protein_intensity_estimation - INFO - prot 5600\n", - "2023-12-04 19:46:48,820 - directlfq.protein_intensity_estimation - INFO - prot 6100\n", - "2023-12-04 19:46:48,954 - directlfq.protein_intensity_estimation - INFO - prot 5300\n", - "2023-12-04 19:46:48,986 - directlfq.protein_intensity_estimation - INFO - prot 6900\n", - "2023-12-04 19:46:49,055 - directlfq.protein_intensity_estimation - INFO - prot 6200\n", - "2023-12-04 19:46:49,129 - directlfq.protein_intensity_estimation - INFO - prot 7200\n", - "2023-12-04 19:46:49,253 - directlfq.protein_intensity_estimation - INFO - prot 6400\n", - "2023-12-04 19:46:49,259 - directlfq.protein_intensity_estimation - INFO - prot 7500\n", - "2023-12-04 19:46:49,399 - directlfq.protein_intensity_estimation - INFO - prot 6700\n", - "2023-12-04 19:46:49,414 - directlfq.protein_intensity_estimation - INFO - prot 7000\n", - "2023-12-04 19:46:49,468 - directlfq.protein_intensity_estimation - INFO - prot 7800\n", - "2023-12-04 19:46:49,526 - directlfq.protein_intensity_estimation - INFO - prot 7300\n", - "2023-12-04 19:46:49,546 - directlfq.protein_intensity_estimation - INFO - prot 8100\n", - "2023-12-04 19:46:49,610 - directlfq.protein_intensity_estimation - INFO - prot 7600\n", - "2023-12-04 19:46:49,622 - directlfq.protein_intensity_estimation - INFO - prot 8400\n", - "2023-12-04 19:46:49,662 - directlfq.protein_intensity_estimation - INFO - prot 7100\n", - "2023-12-04 19:46:49,750 - directlfq.protein_intensity_estimation - INFO - prot 8700\n", - "2023-12-04 19:46:49,781 - directlfq.protein_intensity_estimation - INFO - prot 6500\n", - "2023-12-04 19:46:49,890 - directlfq.protein_intensity_estimation - INFO - prot 9000\n", - "2023-12-04 19:46:49,904 - directlfq.protein_intensity_estimation - INFO - prot 8500\n", - "2023-12-04 19:46:49,913 - directlfq.protein_intensity_estimation - INFO - prot 6800\n", - "2023-12-04 19:46:49,927 - directlfq.protein_intensity_estimation - INFO - prot 8200\n", - "2023-12-04 19:46:49,945 - directlfq.protein_intensity_estimation - INFO - prot 7900\n", - "2023-12-04 19:46:49,960 - directlfq.protein_intensity_estimation - INFO - prot 7400\n", - "2023-12-04 19:46:49,981 - directlfq.protein_intensity_estimation - INFO - prot 7700\n", - "2023-12-04 19:46:50,182 - directlfq.protein_intensity_estimation - INFO - prot 8800\n", - "2023-12-04 19:46:50,202 - directlfq.protein_intensity_estimation - INFO - prot 9300\n", - "2023-12-04 19:46:50,293 - directlfq.protein_intensity_estimation - INFO - prot 9100\n", - "2023-12-04 19:46:50,349 - directlfq.protein_intensity_estimation - INFO - prot 8600\n", - "2023-12-04 19:46:50,351 - directlfq.protein_intensity_estimation - INFO - prot 8000\n", - "2023-12-04 19:46:50,370 - directlfq.protein_intensity_estimation - INFO - prot 8300\n", - "2023-12-04 19:46:50,518 - directlfq.protein_intensity_estimation - INFO - prot 9600\n", - "2023-12-04 19:46:50,566 - directlfq.protein_intensity_estimation - INFO - prot 9400\n", - "2023-12-04 19:46:50,607 - directlfq.protein_intensity_estimation - INFO - prot 9200\n", - "2023-12-04 19:46:50,630 - directlfq.protein_intensity_estimation - INFO - prot 9900\n", - "2023-12-04 19:46:50,631 - directlfq.protein_intensity_estimation - INFO - prot 8900\n", - "2023-12-04 19:46:50,802 - directlfq.protein_intensity_estimation - INFO - prot 10200\n", - "2023-12-04 19:46:50,896 - directlfq.protein_intensity_estimation - INFO - prot 10500\n", - "2023-12-04 19:46:50,915 - directlfq.protein_intensity_estimation - INFO - prot 9700\n", - "2023-12-04 19:46:50,913 - directlfq.protein_intensity_estimation - INFO - prot 9500\n", - "2023-12-04 19:46:50,928 - directlfq.protein_intensity_estimation - INFO - prot 10000\n", - "2023-12-04 19:46:50,981 - directlfq.protein_intensity_estimation - INFO - prot 10800\n", - "2023-12-04 19:46:51,144 - directlfq.protein_intensity_estimation - INFO - prot 10300\n", - "2023-12-04 19:46:51,233 - directlfq.protein_intensity_estimation - INFO - prot 10600\n", - "2023-12-04 19:46:51,262 - directlfq.protein_intensity_estimation - INFO - prot 10100\n", - "2023-12-04 19:46:51,257 - directlfq.protein_intensity_estimation - INFO - prot 9800\n", - "2023-12-04 19:46:51,387 - directlfq.protein_intensity_estimation - INFO - prot 10900\n", - "2023-12-04 19:46:51,304 - directlfq.protein_intensity_estimation - INFO - prot 11400\n", - "2023-12-04 19:46:51,213 - directlfq.protein_intensity_estimation - INFO - prot 11100\n", - "2023-12-04 19:46:51,430 - directlfq.protein_intensity_estimation - INFO - prot 11700\n", - "2023-12-04 19:46:51,515 - directlfq.protein_intensity_estimation - INFO - prot 10700\n", - "2023-12-04 19:46:51,539 - directlfq.protein_intensity_estimation - INFO - prot 10400\n", - "2023-12-04 19:46:51,653 - directlfq.protein_intensity_estimation - INFO - prot 11200\n", - "2023-12-04 19:46:51,659 - directlfq.protein_intensity_estimation - INFO - prot 11000\n", - "2023-12-04 19:46:51,700 - directlfq.protein_intensity_estimation - INFO - prot 11500\n", - "2023-12-04 19:46:51,824 - directlfq.protein_intensity_estimation - INFO - prot 11800\n", - "2023-12-04 19:46:52,000 - directlfq.protein_intensity_estimation - INFO - prot 11300\n", - "2023-12-04 19:46:52,147 - directlfq.protein_intensity_estimation - INFO - prot 11600\n", - "2023-12-04 19:46:52,195 - directlfq.protein_intensity_estimation - INFO - prot 11900\n", - "2023-12-04 19:47:06,301 - directlfq.lfq_manager - INFO - Writing results files.\n", - "2023-12-04 19:47:07,592 - directlfq.lfq_manager - INFO - Analysis finished!\n", - "2023-12-04 19:47:07,607 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", - "2023-12-04 19:47:07,671 - directlfq.utils - INFO - using input type diann_fragion_isotopes\n", - "2023-12-04 19:49:06,218 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", - "2023-12-04 19:49:08,027 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", - "2023-12-04 19:49:08,163 - directlfq.protein_intensity_estimation - INFO - 11983 prots total\n", - "2023-12-04 19:49:08,277 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", - "2023-12-04 19:49:09,653 - directlfq.protein_intensity_estimation - INFO - prot 0\n", - "2023-12-04 19:49:09,865 - directlfq.protein_intensity_estimation - INFO - prot 300\n", - "2023-12-04 19:49:10,196 - directlfq.protein_intensity_estimation - INFO - prot 600\n", - "2023-12-04 19:49:10,429 - directlfq.protein_intensity_estimation - INFO - prot 900\n", - "2023-12-04 19:49:10,600 - directlfq.protein_intensity_estimation - INFO - prot 1200\n", + "2024-01-16 18:16:23,719 - directlfq.protein_intensity_estimation - INFO - lfq-object 2000\n", + "2024-01-16 18:16:23,780 - directlfq.protein_intensity_estimation - INFO - lfq-object 2300\n", + "2024-01-16 18:16:23,882 - directlfq.protein_intensity_estimation - INFO - lfq-object 3100\n", + "2024-01-16 18:16:24,637 - directlfq.protein_intensity_estimation - INFO - lfq-object 2900\n", + "2024-01-16 18:16:25,305 - directlfq.protein_intensity_estimation - INFO - lfq-object 3300\n", + "2024-01-16 18:16:25,728 - directlfq.protein_intensity_estimation - INFO - lfq-object 3600\n", + "2024-01-16 18:16:25,993 - directlfq.protein_intensity_estimation - INFO - lfq-object 3900\n", + "2024-01-16 18:16:26,098 - directlfq.protein_intensity_estimation - INFO - lfq-object 3200\n", + "2024-01-16 18:16:26,323 - directlfq.protein_intensity_estimation - INFO - lfq-object 4200\n", + "2024-01-16 18:16:26,522 - directlfq.protein_intensity_estimation - INFO - lfq-object 4500\n", + "2024-01-16 18:16:26,960 - directlfq.protein_intensity_estimation - INFO - lfq-object 4800\n", + "2024-01-16 18:16:27,199 - directlfq.protein_intensity_estimation - INFO - lfq-object 5100\n", + "2024-01-16 18:16:27,302 - directlfq.protein_intensity_estimation - INFO - lfq-object 3400\n", + "2024-01-16 18:16:27,358 - directlfq.protein_intensity_estimation - INFO - lfq-object 3700\n", + "2024-01-16 18:16:27,392 - directlfq.protein_intensity_estimation - INFO - lfq-object 5400\n", + "2024-01-16 18:16:27,632 - directlfq.protein_intensity_estimation - INFO - lfq-object 5700\n", + "2024-01-16 18:16:28,133 - directlfq.protein_intensity_estimation - INFO - lfq-object 4300\n", + "2024-01-16 18:16:28,204 - directlfq.protein_intensity_estimation - INFO - lfq-object 6000\n", + "2024-01-16 18:16:28,277 - directlfq.protein_intensity_estimation - INFO - lfq-object 4000\n", + "2024-01-16 18:16:28,670 - directlfq.protein_intensity_estimation - INFO - lfq-object 4900\n", + "2024-01-16 18:16:28,981 - directlfq.protein_intensity_estimation - INFO - lfq-object 4600\n", + "2024-01-16 18:16:29,223 - directlfq.protein_intensity_estimation - INFO - lfq-object 3500\n", + "2024-01-16 18:16:29,308 - directlfq.protein_intensity_estimation - INFO - lfq-object 5800\n", + "2024-01-16 18:16:29,339 - directlfq.protein_intensity_estimation - INFO - lfq-object 3800\n", + "2024-01-16 18:16:29,538 - directlfq.protein_intensity_estimation - INFO - lfq-object 5500\n", + "2024-01-16 18:16:29,739 - directlfq.protein_intensity_estimation - INFO - lfq-object 5200\n", + "2024-01-16 18:16:30,163 - directlfq.protein_intensity_estimation - INFO - lfq-object 6100\n", + "2024-01-16 18:16:30,411 - directlfq.protein_intensity_estimation - INFO - lfq-object 4700\n", + "2024-01-16 18:16:30,631 - directlfq.protein_intensity_estimation - INFO - lfq-object 4100\n", + "2024-01-16 18:16:30,677 - directlfq.protein_intensity_estimation - INFO - lfq-object 5900\n", + "2024-01-16 18:16:30,911 - directlfq.protein_intensity_estimation - INFO - lfq-object 5600\n", + "2024-01-16 18:16:30,954 - directlfq.protein_intensity_estimation - INFO - lfq-object 5000\n", + "2024-01-16 18:16:31,027 - directlfq.protein_intensity_estimation - INFO - lfq-object 4400\n", + "2024-01-16 18:16:31,283 - directlfq.protein_intensity_estimation - INFO - lfq-object 6300\n", + "2024-01-16 18:16:31,618 - directlfq.protein_intensity_estimation - INFO - lfq-object 6200\n", + "2024-01-16 18:16:31,798 - directlfq.protein_intensity_estimation - INFO - lfq-object 5300\n", + "2024-01-16 18:16:31,997 - directlfq.protein_intensity_estimation - INFO - lfq-object 6600\n", + "2024-01-16 18:16:32,614 - directlfq.protein_intensity_estimation - INFO - lfq-object 6900\n", + "2024-01-16 18:16:32,843 - directlfq.protein_intensity_estimation - INFO - lfq-object 7200\n", + "2024-01-16 18:16:33,163 - directlfq.protein_intensity_estimation - INFO - lfq-object 7500\n", + "2024-01-16 18:16:33,570 - directlfq.protein_intensity_estimation - INFO - lfq-object 7800\n", + "2024-01-16 18:16:34,101 - directlfq.protein_intensity_estimation - INFO - lfq-object 6400\n", + "2024-01-16 18:16:34,169 - directlfq.protein_intensity_estimation - INFO - lfq-object 8100\n", + "2024-01-16 18:16:34,486 - directlfq.protein_intensity_estimation - INFO - lfq-object 8400\n", + "2024-01-16 18:16:34,786 - directlfq.protein_intensity_estimation - INFO - lfq-object 7000\n", + "2024-01-16 18:16:34,807 - directlfq.protein_intensity_estimation - INFO - lfq-object 8700\n", + "2024-01-16 18:16:34,803 - directlfq.protein_intensity_estimation - INFO - lfq-object 6700\n", + "2024-01-16 18:16:35,093 - directlfq.protein_intensity_estimation - INFO - lfq-object 9000\n", + "2024-01-16 18:16:35,129 - directlfq.protein_intensity_estimation - INFO - lfq-object 7300\n", + "2024-01-16 18:16:35,210 - directlfq.protein_intensity_estimation - INFO - lfq-object 7600\n", + "2024-01-16 18:16:35,918 - directlfq.protein_intensity_estimation - INFO - lfq-object 7900\n", + "2024-01-16 18:16:36,379 - directlfq.protein_intensity_estimation - INFO - lfq-object 8500\n", + "2024-01-16 18:16:36,448 - directlfq.protein_intensity_estimation - INFO - lfq-object 8200\n", + "2024-01-16 18:16:36,578 - directlfq.protein_intensity_estimation - INFO - lfq-object 7100\n", + "2024-01-16 18:16:36,751 - directlfq.protein_intensity_estimation - INFO - lfq-object 6500\n", + "2024-01-16 18:16:36,811 - directlfq.protein_intensity_estimation - INFO - lfq-object 8800\n", + "2024-01-16 18:16:37,258 - directlfq.protein_intensity_estimation - INFO - lfq-object 7700\n", + "2024-01-16 18:16:37,305 - directlfq.protein_intensity_estimation - INFO - lfq-object 9100\n", + "2024-01-16 18:16:37,451 - directlfq.protein_intensity_estimation - INFO - lfq-object 7400\n", + "2024-01-16 18:16:37,606 - directlfq.protein_intensity_estimation - INFO - lfq-object 6800\n", + "2024-01-16 18:16:38,181 - directlfq.protein_intensity_estimation - INFO - lfq-object 8000\n", + "2024-01-16 18:16:38,716 - directlfq.protein_intensity_estimation - INFO - lfq-object 8600\n", + "2024-01-16 18:16:38,739 - directlfq.protein_intensity_estimation - INFO - lfq-object 8300\n", + "2024-01-16 18:16:38,828 - directlfq.protein_intensity_estimation - INFO - lfq-object 9300\n", + "2024-01-16 18:16:39,104 - directlfq.protein_intensity_estimation - INFO - lfq-object 8900\n", + "2024-01-16 18:16:39,377 - directlfq.protein_intensity_estimation - INFO - lfq-object 9600\n", + "2024-01-16 18:16:39,437 - directlfq.protein_intensity_estimation - INFO - lfq-object 9200\n", + "2024-01-16 18:16:40,261 - directlfq.protein_intensity_estimation - INFO - lfq-object 9900\n", + "2024-01-16 18:16:40,863 - directlfq.protein_intensity_estimation - INFO - lfq-object 9400\n", + "2024-01-16 18:16:40,902 - directlfq.protein_intensity_estimation - INFO - lfq-object 10200\n", + "2024-01-16 18:16:41,171 - directlfq.protein_intensity_estimation - INFO - lfq-object 10500\n", + "2024-01-16 18:16:41,407 - directlfq.protein_intensity_estimation - INFO - lfq-object 10800\n", + "2024-01-16 18:16:41,642 - directlfq.protein_intensity_estimation - INFO - lfq-object 11100\n", + "2024-01-16 18:16:41,642 - directlfq.protein_intensity_estimation - INFO - lfq-object 9700\n", + "2024-01-16 18:16:41,891 - directlfq.protein_intensity_estimation - INFO - lfq-object 11400\n", + "2024-01-16 18:16:41,986 - directlfq.protein_intensity_estimation - INFO - lfq-object 10000\n", + "2024-01-16 18:16:42,471 - directlfq.protein_intensity_estimation - INFO - lfq-object 11700\n", + "2024-01-16 18:16:42,752 - directlfq.protein_intensity_estimation - INFO - lfq-object 9500\n", + "2024-01-16 18:16:42,841 - directlfq.protein_intensity_estimation - INFO - lfq-object 10300\n", + "2024-01-16 18:16:43,050 - directlfq.protein_intensity_estimation - INFO - lfq-object 10600\n", + "2024-01-16 18:16:43,567 - directlfq.protein_intensity_estimation - INFO - lfq-object 10900\n", + "2024-01-16 18:16:43,604 - directlfq.protein_intensity_estimation - INFO - lfq-object 9800\n", + "2024-01-16 18:16:43,859 - directlfq.protein_intensity_estimation - INFO - lfq-object 11200\n", + "2024-01-16 18:16:43,987 - directlfq.protein_intensity_estimation - INFO - lfq-object 10100\n", + "2024-01-16 18:16:44,057 - directlfq.protein_intensity_estimation - INFO - lfq-object 11500\n", + "2024-01-16 18:16:44,650 - directlfq.protein_intensity_estimation - INFO - lfq-object 11800\n", + "2024-01-16 18:16:44,799 - directlfq.protein_intensity_estimation - INFO - lfq-object 10700\n", + "2024-01-16 18:16:44,867 - directlfq.protein_intensity_estimation - INFO - lfq-object 10400\n", + "2024-01-16 18:16:45,361 - directlfq.protein_intensity_estimation - INFO - lfq-object 11000\n", + "2024-01-16 18:16:45,879 - directlfq.protein_intensity_estimation - INFO - lfq-object 11300\n", + "2024-01-16 18:16:46,263 - directlfq.protein_intensity_estimation - INFO - lfq-object 11600\n", + "2024-01-16 18:16:46,609 - directlfq.protein_intensity_estimation - INFO - lfq-object 11900\n", + "2024-01-16 18:16:53,096 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:16:58,552 - directlfq.lfq_manager - INFO - Analysis finished!\n", + "2024-01-16 18:16:58,608 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:16:58,712 - directlfq.utils - INFO - using input type diann_precursor_ms1_and_ms2\n", + "2024-01-16 18:17:12,720 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:17:13,037 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:17:13,059 - directlfq.protein_intensity_estimation - INFO - 11983 lfq-objects total\n", + "2024-01-16 18:17:16,224 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:17:16,296 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", + "2024-01-16 18:17:16,466 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:17:16,615 - directlfq.protein_intensity_estimation - INFO - lfq-object 300\n", + "2024-01-16 18:17:16,974 - directlfq.protein_intensity_estimation - INFO - lfq-object 600\n", + "2024-01-16 18:17:17,218 - directlfq.protein_intensity_estimation - INFO - lfq-object 900\n", + "2024-01-16 18:17:17,262 - directlfq.protein_intensity_estimation - INFO - lfq-object 1200\n", + "2024-01-16 18:17:17,408 - directlfq.protein_intensity_estimation - INFO - lfq-object 1500\n", + "2024-01-16 18:17:17,491 - directlfq.protein_intensity_estimation - INFO - lfq-object 100\n", + "2024-01-16 18:17:17,564 - directlfq.protein_intensity_estimation - INFO - lfq-object 1800\n", + "2024-01-16 18:17:17,712 - directlfq.protein_intensity_estimation - INFO - lfq-object 2100\n", + "2024-01-16 18:17:17,914 - directlfq.protein_intensity_estimation - INFO - lfq-object 2400\n", + "2024-01-16 18:17:18,138 - directlfq.protein_intensity_estimation - INFO - lfq-object 2700\n", + "2024-01-16 18:17:18,197 - directlfq.protein_intensity_estimation - INFO - lfq-object 200\n", + "2024-01-16 18:17:18,244 - directlfq.protein_intensity_estimation - INFO - lfq-object 400\n", + "2024-01-16 18:17:18,452 - directlfq.protein_intensity_estimation - INFO - lfq-object 700\n", + "2024-01-16 18:17:18,888 - directlfq.protein_intensity_estimation - INFO - lfq-object 1000\n", + "2024-01-16 18:17:19,044 - directlfq.protein_intensity_estimation - INFO - lfq-object 1600\n", + "2024-01-16 18:17:19,053 - directlfq.protein_intensity_estimation - INFO - lfq-object 1300\n", + "2024-01-16 18:17:19,340 - directlfq.protein_intensity_estimation - INFO - lfq-object 3000\n", + "2024-01-16 18:17:19,508 - directlfq.protein_intensity_estimation - INFO - lfq-object 2500\n", + "2024-01-16 18:17:19,518 - directlfq.protein_intensity_estimation - INFO - lfq-object 1900\n", + "2024-01-16 18:17:19,543 - directlfq.protein_intensity_estimation - INFO - lfq-object 2200\n", + "2024-01-16 18:17:19,682 - directlfq.protein_intensity_estimation - INFO - lfq-object 500\n", + "2024-01-16 18:17:19,949 - directlfq.protein_intensity_estimation - INFO - lfq-object 2800\n", + "2024-01-16 18:17:20,178 - directlfq.protein_intensity_estimation - INFO - lfq-object 800\n", + "2024-01-16 18:17:20,278 - directlfq.protein_intensity_estimation - INFO - lfq-object 1400\n", + "2024-01-16 18:17:20,318 - directlfq.protein_intensity_estimation - INFO - lfq-object 1100\n", + "2024-01-16 18:17:20,458 - directlfq.protein_intensity_estimation - INFO - lfq-object 2600\n", + "2024-01-16 18:17:20,501 - directlfq.protein_intensity_estimation - INFO - lfq-object 3100\n", + "2024-01-16 18:17:20,680 - directlfq.protein_intensity_estimation - INFO - lfq-object 1700\n", + "2024-01-16 18:17:20,910 - directlfq.protein_intensity_estimation - INFO - lfq-object 2300\n", + "2024-01-16 18:17:21,037 - directlfq.protein_intensity_estimation - INFO - lfq-object 2000\n", + "2024-01-16 18:17:21,484 - directlfq.protein_intensity_estimation - INFO - lfq-object 2900\n", + "2024-01-16 18:17:21,804 - directlfq.protein_intensity_estimation - INFO - lfq-object 3300\n", + "2024-01-16 18:17:21,996 - directlfq.protein_intensity_estimation - INFO - lfq-object 3200\n", + "2024-01-16 18:17:22,413 - directlfq.protein_intensity_estimation - INFO - lfq-object 3600\n", + "2024-01-16 18:17:22,619 - directlfq.protein_intensity_estimation - INFO - lfq-object 3900\n", + "2024-01-16 18:17:22,979 - directlfq.protein_intensity_estimation - INFO - lfq-object 3400\n", + "2024-01-16 18:17:23,061 - directlfq.protein_intensity_estimation - INFO - lfq-object 4200\n", + "2024-01-16 18:17:23,253 - directlfq.protein_intensity_estimation - INFO - lfq-object 4500\n", + "2024-01-16 18:17:23,288 - directlfq.protein_intensity_estimation - INFO - lfq-object 3700\n", + "2024-01-16 18:17:23,449 - directlfq.protein_intensity_estimation - INFO - lfq-object 4800\n", + "2024-01-16 18:17:23,623 - directlfq.protein_intensity_estimation - INFO - lfq-object 5100\n", + "2024-01-16 18:17:23,733 - directlfq.protein_intensity_estimation - INFO - lfq-object 4000\n", + "2024-01-16 18:17:23,764 - directlfq.protein_intensity_estimation - INFO - lfq-object 5400\n", + "2024-01-16 18:17:23,790 - directlfq.protein_intensity_estimation - INFO - lfq-object 3500\n", + "2024-01-16 18:17:23,988 - directlfq.protein_intensity_estimation - INFO - lfq-object 4300\n", + "2024-01-16 18:17:24,143 - directlfq.protein_intensity_estimation - INFO - lfq-object 3800\n", + "2024-01-16 18:17:24,270 - directlfq.protein_intensity_estimation - INFO - lfq-object 5700\n", + "2024-01-16 18:17:24,289 - directlfq.protein_intensity_estimation - INFO - lfq-object 4900\n", + "2024-01-16 18:17:24,440 - directlfq.protein_intensity_estimation - INFO - lfq-object 6000\n", + "2024-01-16 18:17:24,591 - directlfq.protein_intensity_estimation - INFO - lfq-object 4600\n", + "2024-01-16 18:17:24,892 - directlfq.protein_intensity_estimation - INFO - lfq-object 5500\n", + "2024-01-16 18:17:24,960 - directlfq.protein_intensity_estimation - INFO - lfq-object 6300\n", + "2024-01-16 18:17:25,101 - directlfq.protein_intensity_estimation - INFO - lfq-object 5200\n", + "2024-01-16 18:17:25,177 - directlfq.protein_intensity_estimation - INFO - lfq-object 5800\n", + "2024-01-16 18:17:25,229 - directlfq.protein_intensity_estimation - INFO - lfq-object 4100\n", + "2024-01-16 18:17:25,276 - directlfq.protein_intensity_estimation - INFO - lfq-object 6600\n", + "2024-01-16 18:17:25,384 - directlfq.protein_intensity_estimation - INFO - lfq-object 4700\n", + "2024-01-16 18:17:25,543 - directlfq.protein_intensity_estimation - INFO - lfq-object 6100\n", + "2024-01-16 18:17:25,683 - directlfq.protein_intensity_estimation - INFO - lfq-object 5600\n", + "2024-01-16 18:17:25,756 - directlfq.protein_intensity_estimation - INFO - lfq-object 4400\n", + "2024-01-16 18:17:25,818 - directlfq.protein_intensity_estimation - INFO - lfq-object 5000\n", + "2024-01-16 18:17:26,030 - directlfq.protein_intensity_estimation - INFO - lfq-object 5900\n", + "2024-01-16 18:17:26,410 - directlfq.protein_intensity_estimation - INFO - lfq-object 6200\n", + "2024-01-16 18:17:26,527 - directlfq.protein_intensity_estimation - INFO - lfq-object 5300\n", + "2024-01-16 18:17:26,601 - directlfq.protein_intensity_estimation - INFO - lfq-object 6900\n", + "2024-01-16 18:17:26,818 - directlfq.protein_intensity_estimation - INFO - lfq-object 7200\n", + "2024-01-16 18:17:26,876 - directlfq.protein_intensity_estimation - INFO - lfq-object 6400\n", + "2024-01-16 18:17:27,446 - directlfq.protein_intensity_estimation - INFO - lfq-object 6700\n", + "2024-01-16 18:17:27,582 - directlfq.protein_intensity_estimation - INFO - lfq-object 7500\n", + "2024-01-16 18:17:27,612 - directlfq.protein_intensity_estimation - INFO - lfq-object 7800\n", + "2024-01-16 18:17:27,779 - directlfq.protein_intensity_estimation - INFO - lfq-object 8100\n", + "2024-01-16 18:17:27,933 - directlfq.protein_intensity_estimation - INFO - lfq-object 7000\n", + "2024-01-16 18:17:27,995 - directlfq.protein_intensity_estimation - INFO - lfq-object 8400\n", + "2024-01-16 18:17:28,214 - directlfq.protein_intensity_estimation - INFO - lfq-object 7300\n", + "2024-01-16 18:17:28,262 - directlfq.protein_intensity_estimation - INFO - lfq-object 8700\n", + "2024-01-16 18:17:28,514 - directlfq.protein_intensity_estimation - INFO - lfq-object 6500\n", + "2024-01-16 18:17:28,549 - directlfq.protein_intensity_estimation - INFO - lfq-object 9000\n", + "2024-01-16 18:17:28,840 - directlfq.protein_intensity_estimation - INFO - lfq-object 7600\n", + "2024-01-16 18:17:28,978 - directlfq.protein_intensity_estimation - INFO - lfq-object 7100\n", + "2024-01-16 18:17:29,144 - directlfq.protein_intensity_estimation - INFO - lfq-object 8500\n", + "2024-01-16 18:17:29,178 - directlfq.protein_intensity_estimation - INFO - lfq-object 6800\n", + "2024-01-16 18:17:29,265 - directlfq.protein_intensity_estimation - INFO - lfq-object 7900\n", + "2024-01-16 18:17:29,330 - directlfq.protein_intensity_estimation - INFO - lfq-object 8200\n", + "2024-01-16 18:17:29,656 - directlfq.protein_intensity_estimation - INFO - lfq-object 8800\n", + "2024-01-16 18:17:29,708 - directlfq.protein_intensity_estimation - INFO - lfq-object 7400\n", + "2024-01-16 18:17:29,998 - directlfq.protein_intensity_estimation - INFO - lfq-object 9100\n", + "2024-01-16 18:17:30,072 - directlfq.protein_intensity_estimation - INFO - lfq-object 7700\n", + "2024-01-16 18:17:30,490 - directlfq.protein_intensity_estimation - INFO - lfq-object 9300\n", + "2024-01-16 18:17:30,547 - directlfq.protein_intensity_estimation - INFO - lfq-object 8600\n", + "2024-01-16 18:17:30,577 - directlfq.protein_intensity_estimation - INFO - lfq-object 8000\n", + "2024-01-16 18:17:30,699 - directlfq.protein_intensity_estimation - INFO - lfq-object 8300\n", + "2024-01-16 18:17:30,986 - directlfq.protein_intensity_estimation - INFO - lfq-object 8900\n", + "2024-01-16 18:17:31,055 - directlfq.protein_intensity_estimation - INFO - lfq-object 9600\n", + "2024-01-16 18:17:31,248 - directlfq.protein_intensity_estimation - INFO - lfq-object 9200\n", + "2024-01-16 18:17:31,294 - directlfq.protein_intensity_estimation - INFO - lfq-object 9900\n", + "2024-01-16 18:17:31,612 - directlfq.protein_intensity_estimation - INFO - lfq-object 10200\n", + "2024-01-16 18:17:31,646 - directlfq.protein_intensity_estimation - INFO - lfq-object 9400\n", + "2024-01-16 18:17:31,777 - directlfq.protein_intensity_estimation - INFO - lfq-object 10500\n", + "2024-01-16 18:17:32,257 - directlfq.protein_intensity_estimation - INFO - lfq-object 10800\n", + "2024-01-16 18:17:32,577 - directlfq.protein_intensity_estimation - INFO - lfq-object 10000\n", + "2024-01-16 18:17:32,587 - directlfq.protein_intensity_estimation - INFO - lfq-object 11100\n", + "2024-01-16 18:17:32,640 - directlfq.protein_intensity_estimation - INFO - lfq-object 9700\n", + "2024-01-16 18:17:32,953 - directlfq.protein_intensity_estimation - INFO - lfq-object 11400\n", + "2024-01-16 18:17:33,009 - directlfq.protein_intensity_estimation - INFO - lfq-object 10300\n", + "2024-01-16 18:17:33,003 - directlfq.protein_intensity_estimation - INFO - lfq-object 9500\n", + "2024-01-16 18:17:33,081 - directlfq.protein_intensity_estimation - INFO - lfq-object 10600\n", + "2024-01-16 18:17:33,477 - directlfq.protein_intensity_estimation - INFO - lfq-object 11700\n", + "2024-01-16 18:17:33,721 - directlfq.protein_intensity_estimation - INFO - lfq-object 10900\n", + "2024-01-16 18:17:33,830 - directlfq.protein_intensity_estimation - INFO - lfq-object 10100\n", + "2024-01-16 18:17:33,876 - directlfq.protein_intensity_estimation - INFO - lfq-object 11200\n", + "2024-01-16 18:17:33,894 - directlfq.protein_intensity_estimation - INFO - lfq-object 9800\n", + "2024-01-16 18:17:34,271 - directlfq.protein_intensity_estimation - INFO - lfq-object 10700\n", + "2024-01-16 18:17:34,310 - directlfq.protein_intensity_estimation - INFO - lfq-object 11500\n", + "2024-01-16 18:17:34,339 - directlfq.protein_intensity_estimation - INFO - lfq-object 10400\n", + "2024-01-16 18:17:34,875 - directlfq.protein_intensity_estimation - INFO - lfq-object 11000\n", + "2024-01-16 18:17:34,882 - directlfq.protein_intensity_estimation - INFO - lfq-object 11800\n", + "2024-01-16 18:17:35,178 - directlfq.protein_intensity_estimation - INFO - lfq-object 11300\n", + "2024-01-16 18:17:35,746 - directlfq.protein_intensity_estimation - INFO - lfq-object 11600\n", + "2024-01-16 18:17:36,104 - directlfq.protein_intensity_estimation - INFO - lfq-object 11900\n", + "2024-01-16 18:17:41,620 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:17:44,534 - directlfq.lfq_manager - INFO - Analysis finished!\n", + "2024-01-16 18:17:44,569 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:17:44,638 - directlfq.utils - INFO - using input type diann_precursors\n", + "2024-01-16 18:17:50,377 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:17:50,548 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:17:50,561 - directlfq.protein_intensity_estimation - INFO - 11983 lfq-objects total\n", + "2024-01-16 18:17:53,623 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:17:53,691 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", + "2024-01-16 18:17:54,037 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:17:54,172 - directlfq.protein_intensity_estimation - INFO - lfq-object 300\n", + "2024-01-16 18:17:54,306 - directlfq.protein_intensity_estimation - INFO - lfq-object 600\n", + "2024-01-16 18:17:54,441 - directlfq.protein_intensity_estimation - INFO - lfq-object 900\n", + "2024-01-16 18:17:54,576 - directlfq.protein_intensity_estimation - INFO - lfq-object 1200\n", + "2024-01-16 18:17:54,707 - directlfq.protein_intensity_estimation - INFO - lfq-object 1500\n", + "2024-01-16 18:17:54,886 - directlfq.protein_intensity_estimation - INFO - lfq-object 1800\n", + "2024-01-16 18:17:54,993 - directlfq.protein_intensity_estimation - INFO - lfq-object 100\n", + "2024-01-16 18:17:55,022 - directlfq.protein_intensity_estimation - INFO - lfq-object 2100\n", + "2024-01-16 18:17:55,336 - directlfq.protein_intensity_estimation - INFO - lfq-object 200\n", + "2024-01-16 18:17:55,433 - directlfq.protein_intensity_estimation - INFO - lfq-object 700\n", + "2024-01-16 18:17:55,483 - directlfq.protein_intensity_estimation - INFO - lfq-object 400\n", + "2024-01-16 18:17:55,555 - directlfq.protein_intensity_estimation - INFO - lfq-object 2400\n", + "2024-01-16 18:17:55,766 - directlfq.protein_intensity_estimation - INFO - lfq-object 2700\n", + "2024-01-16 18:17:55,908 - directlfq.protein_intensity_estimation - INFO - lfq-object 1300\n", + "2024-01-16 18:17:55,921 - directlfq.protein_intensity_estimation - INFO - lfq-object 1000\n", + "2024-01-16 18:17:56,016 - directlfq.protein_intensity_estimation - INFO - lfq-object 1600\n", + "2024-01-16 18:17:56,117 - directlfq.protein_intensity_estimation - INFO - lfq-object 3000\n", + "2024-01-16 18:17:56,224 - directlfq.protein_intensity_estimation - INFO - lfq-object 1900\n", + "2024-01-16 18:17:56,331 - directlfq.protein_intensity_estimation - INFO - lfq-object 500\n", + "2024-01-16 18:17:56,344 - directlfq.protein_intensity_estimation - INFO - lfq-object 2200\n", + "2024-01-16 18:17:56,573 - directlfq.protein_intensity_estimation - INFO - lfq-object 800\n", + "2024-01-16 18:17:56,638 - directlfq.protein_intensity_estimation - INFO - lfq-object 1400\n", + "2024-01-16 18:17:56,727 - 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INFO - lfq-object 3600\n", + "2024-01-16 18:17:58,119 - directlfq.protein_intensity_estimation - INFO - lfq-object 2900\n", + "2024-01-16 18:17:58,323 - directlfq.protein_intensity_estimation - INFO - lfq-object 3900\n", + "2024-01-16 18:17:58,352 - directlfq.protein_intensity_estimation - INFO - lfq-object 3400\n", + "2024-01-16 18:17:58,421 - directlfq.protein_intensity_estimation - INFO - lfq-object 3700\n", + "2024-01-16 18:17:58,496 - directlfq.protein_intensity_estimation - INFO - lfq-object 4200\n", + "2024-01-16 18:17:58,689 - directlfq.protein_intensity_estimation - INFO - lfq-object 4500\n", + "2024-01-16 18:17:58,727 - directlfq.protein_intensity_estimation - INFO - lfq-object 3500\n", + "2024-01-16 18:17:58,845 - directlfq.protein_intensity_estimation - INFO - lfq-object 3800\n", + "2024-01-16 18:17:58,876 - directlfq.protein_intensity_estimation - INFO - lfq-object 4800\n", + "2024-01-16 18:17:59,005 - directlfq.protein_intensity_estimation - INFO - lfq-object 4300\n", + "2024-01-16 18:17:58,961 - directlfq.protein_intensity_estimation - INFO - lfq-object 4000\n", + "2024-01-16 18:17:59,266 - directlfq.protein_intensity_estimation - INFO - lfq-object 5100\n", + "2024-01-16 18:17:59,284 - directlfq.protein_intensity_estimation - INFO - lfq-object 4900\n", + "2024-01-16 18:17:59,435 - directlfq.protein_intensity_estimation - INFO - lfq-object 4600\n", + "2024-01-16 18:17:59,451 - directlfq.protein_intensity_estimation - INFO - lfq-object 5400\n", + "2024-01-16 18:17:59,589 - directlfq.protein_intensity_estimation - INFO - lfq-object 5700\n", + "2024-01-16 18:17:59,715 - directlfq.protein_intensity_estimation - INFO - lfq-object 4100\n", + "2024-01-16 18:17:59,760 - directlfq.protein_intensity_estimation - INFO - lfq-object 4700\n", + "2024-01-16 18:17:59,726 - directlfq.protein_intensity_estimation - INFO - lfq-object 6000\n", + "2024-01-16 18:17:59,962 - directlfq.protein_intensity_estimation - INFO - lfq-object 5500\n", + "2024-01-16 18:17:59,976 - directlfq.protein_intensity_estimation - INFO - lfq-object 5800\n", + "2024-01-16 18:17:59,983 - directlfq.protein_intensity_estimation - INFO - lfq-object 4400\n", + "2024-01-16 18:17:59,985 - directlfq.protein_intensity_estimation - INFO - lfq-object 6300\n", + "2024-01-16 18:18:00,004 - directlfq.protein_intensity_estimation - INFO - lfq-object 5200\n", + "2024-01-16 18:18:00,045 - directlfq.protein_intensity_estimation - INFO - lfq-object 5000\n", + "2024-01-16 18:18:00,254 - directlfq.protein_intensity_estimation - INFO - lfq-object 6600\n", + "2024-01-16 18:18:00,299 - directlfq.protein_intensity_estimation - INFO - lfq-object 6100\n", + "2024-01-16 18:18:00,423 - directlfq.protein_intensity_estimation - INFO - lfq-object 5900\n", + "2024-01-16 18:18:00,613 - directlfq.protein_intensity_estimation - INFO - lfq-object 5600\n", + "2024-01-16 18:18:00,754 - directlfq.protein_intensity_estimation - INFO - lfq-object 6200\n", + "2024-01-16 18:18:00,802 - directlfq.protein_intensity_estimation - INFO - lfq-object 6900\n", + "2024-01-16 18:18:00,903 - 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INFO - lfq-object 7100\n", + "2024-01-16 18:18:01,975 - directlfq.protein_intensity_estimation - INFO - lfq-object 7600\n", + "2024-01-16 18:18:02,427 - directlfq.protein_intensity_estimation - INFO - lfq-object 6500\n", + "2024-01-16 18:18:02,471 - directlfq.protein_intensity_estimation - INFO - lfq-object 8200\n", + "2024-01-16 18:18:02,482 - directlfq.protein_intensity_estimation - INFO - lfq-object 8500\n", + "2024-01-16 18:18:02,589 - directlfq.protein_intensity_estimation - INFO - lfq-object 7900\n", + "2024-01-16 18:18:02,653 - directlfq.protein_intensity_estimation - INFO - lfq-object 8700\n", + "2024-01-16 18:18:02,825 - directlfq.protein_intensity_estimation - INFO - lfq-object 7400\n", + "2024-01-16 18:18:02,890 - directlfq.protein_intensity_estimation - INFO - lfq-object 7700\n", + "2024-01-16 18:18:02,927 - directlfq.protein_intensity_estimation - INFO - lfq-object 6800\n", + "2024-01-16 18:18:02,946 - directlfq.protein_intensity_estimation - INFO - lfq-object 9000\n", + "2024-01-16 18:18:03,207 - directlfq.protein_intensity_estimation - INFO - lfq-object 9300\n", + "2024-01-16 18:18:03,353 - directlfq.protein_intensity_estimation - INFO - lfq-object 8000\n", + "2024-01-16 18:18:03,437 - directlfq.protein_intensity_estimation - INFO - lfq-object 8800\n", + "2024-01-16 18:18:03,554 - directlfq.protein_intensity_estimation - INFO - lfq-object 8300\n", + "2024-01-16 18:18:03,598 - directlfq.protein_intensity_estimation - INFO - lfq-object 8600\n", + "2024-01-16 18:18:03,780 - directlfq.protein_intensity_estimation - INFO - lfq-object 9600\n", + "2024-01-16 18:18:03,909 - directlfq.protein_intensity_estimation - INFO - lfq-object 9400\n", + "2024-01-16 18:18:03,983 - directlfq.protein_intensity_estimation - INFO - lfq-object 9100\n", + "2024-01-16 18:18:04,125 - directlfq.protein_intensity_estimation - INFO - lfq-object 9900\n", + "2024-01-16 18:18:04,156 - directlfq.protein_intensity_estimation - INFO - lfq-object 8900\n", + "2024-01-16 18:18:04,497 - directlfq.protein_intensity_estimation - INFO - lfq-object 9700\n", + "2024-01-16 18:18:04,516 - directlfq.protein_intensity_estimation - INFO - lfq-object 9200\n", + "2024-01-16 18:18:04,526 - directlfq.protein_intensity_estimation - INFO - lfq-object 9500\n", + "2024-01-16 18:18:04,664 - directlfq.protein_intensity_estimation - INFO - lfq-object 10200\n", + "2024-01-16 18:18:04,677 - directlfq.protein_intensity_estimation - INFO - lfq-object 10000\n", + "2024-01-16 18:18:04,850 - directlfq.protein_intensity_estimation - INFO - lfq-object 10500\n", + "2024-01-16 18:18:04,991 - directlfq.protein_intensity_estimation - INFO - lfq-object 10800\n", + "2024-01-16 18:18:05,179 - directlfq.protein_intensity_estimation - INFO - lfq-object 9800\n", + "2024-01-16 18:18:05,235 - directlfq.protein_intensity_estimation - INFO - lfq-object 11100\n", + "2024-01-16 18:18:05,335 - directlfq.protein_intensity_estimation - INFO - lfq-object 10300\n", + "2024-01-16 18:18:05,351 - directlfq.protein_intensity_estimation - INFO - lfq-object 10100\n", + "2024-01-16 18:18:05,429 - directlfq.protein_intensity_estimation - INFO - lfq-object 11400\n", + "2024-01-16 18:18:05,535 - directlfq.protein_intensity_estimation - INFO - lfq-object 10600\n", + "2024-01-16 18:18:05,577 - directlfq.protein_intensity_estimation - INFO - lfq-object 11700\n", + "2024-01-16 18:18:05,815 - directlfq.protein_intensity_estimation - INFO - lfq-object 10900\n", + "2024-01-16 18:18:05,929 - directlfq.protein_intensity_estimation - INFO - lfq-object 11200\n", + "2024-01-16 18:18:06,040 - directlfq.protein_intensity_estimation - INFO - lfq-object 10400\n", + "2024-01-16 18:18:06,124 - directlfq.protein_intensity_estimation - INFO - lfq-object 10700\n", + "2024-01-16 18:18:06,209 - directlfq.protein_intensity_estimation - INFO - lfq-object 11500\n", + "2024-01-16 18:18:06,354 - directlfq.protein_intensity_estimation - INFO - lfq-object 11800\n", + "2024-01-16 18:18:06,386 - directlfq.protein_intensity_estimation - INFO - lfq-object 11000\n", + "2024-01-16 18:18:06,621 - directlfq.protein_intensity_estimation - INFO - lfq-object 11300\n", + "2024-01-16 18:18:07,055 - directlfq.protein_intensity_estimation - INFO - lfq-object 11900\n", + "2024-01-16 18:18:07,072 - directlfq.protein_intensity_estimation - INFO - lfq-object 11600\n", + "2024-01-16 18:18:11,989 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:18:13,426 - directlfq.lfq_manager - INFO - Analysis finished!\n", + "2024-01-16 18:18:13,446 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n", + "2024-01-16 18:18:13,513 - directlfq.utils - INFO - using input type diann_fragion_isotopes\n", + "2024-01-16 18:19:25,977 - directlfq.lfq_manager - INFO - Performing sample normalization.\n", + "2024-01-16 18:19:27,763 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n", + "2024-01-16 18:19:27,896 - directlfq.protein_intensity_estimation - INFO - 11983 lfq-objects total\n", + "2024-01-16 18:19:31,839 - directlfq.protein_intensity_estimation - INFO - Split up normed_df into individual lfq-objects\n", + "2024-01-16 18:19:31,950 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n", + "2024-01-16 18:19:32,222 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n", + "2024-01-16 18:19:32,552 - directlfq.protein_intensity_estimation - INFO - lfq-object 300\n", + "2024-01-16 18:19:32,976 - directlfq.protein_intensity_estimation - INFO - lfq-object 600\n", + "2024-01-16 18:19:33,311 - directlfq.protein_intensity_estimation - INFO - lfq-object 900\n", + "2024-01-16 18:19:33,548 - directlfq.protein_intensity_estimation - INFO - lfq-object 1200\n", + "2024-01-16 18:19:33,820 - directlfq.protein_intensity_estimation - INFO - lfq-object 1500\n", + "2024-01-16 18:19:34,055 - directlfq.protein_intensity_estimation - INFO - lfq-object 1800\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:49:10,792 - directlfq.protein_intensity_estimation - INFO - prot 1500\n", - "2023-12-04 19:49:10,899 - directlfq.protein_intensity_estimation - INFO - prot 1800\n", - "2023-12-04 19:49:11,231 - directlfq.protein_intensity_estimation - INFO - prot 2100\n", - "2023-12-04 19:49:11,320 - directlfq.protein_intensity_estimation - INFO - prot 2400\n", - "2023-12-04 19:49:11,369 - directlfq.protein_intensity_estimation - INFO - prot 100\n", + "2024-01-16 18:19:34,878 - directlfq.protein_intensity_estimation - INFO - lfq-object 2100\n", + "2024-01-16 18:19:35,149 - directlfq.protein_intensity_estimation - INFO - lfq-object 2400\n", + "2024-01-16 18:19:35,785 - directlfq.protein_intensity_estimation - INFO - lfq-object 2700\n", + "2024-01-16 18:19:35,748 - directlfq.protein_intensity_estimation - INFO - lfq-object 100\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:49:11,821 - directlfq.protein_intensity_estimation - INFO - prot 2700\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:49:12,244 - directlfq.protein_intensity_estimation - INFO - prot 400\n", - "2023-12-04 19:49:12,367 - directlfq.protein_intensity_estimation - INFO - prot 700\n", + "2024-01-16 18:19:37,469 - directlfq.protein_intensity_estimation - INFO - lfq-object 400\n", + "2024-01-16 18:19:37,927 - directlfq.protein_intensity_estimation - INFO - lfq-object 700\n", + "2024-01-16 18:19:38,972 - directlfq.protein_intensity_estimation - INFO - lfq-object 1000\n", + "2024-01-16 18:19:39,046 - directlfq.protein_intensity_estimation - INFO - lfq-object 1600\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:49:12,827 - directlfq.protein_intensity_estimation - INFO - prot 1000\n", - "2023-12-04 19:49:12,957 - directlfq.protein_intensity_estimation - INFO - prot 200\n", - "2023-12-04 19:49:13,019 - directlfq.protein_intensity_estimation - INFO - prot 1600\n", - "2023-12-04 19:49:13,026 - directlfq.protein_intensity_estimation - INFO - prot 1300\n", + "2024-01-16 18:19:39,318 - directlfq.protein_intensity_estimation - INFO - lfq-object 1300\n", + "2024-01-16 18:19:39,687 - directlfq.protein_intensity_estimation - INFO - lfq-object 200\n", + "2024-01-16 18:19:40,015 - directlfq.protein_intensity_estimation - INFO - lfq-object 1900\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:49:13,451 - directlfq.protein_intensity_estimation - INFO - prot 1900\n", - "2023-12-04 19:49:13,724 - directlfq.protein_intensity_estimation - INFO - prot 2200\n", - "2023-12-04 19:49:13,851 - directlfq.protein_intensity_estimation - INFO - prot 2500\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:19:40,637 - directlfq.protein_intensity_estimation - INFO - lfq-object 2200\n", + "2024-01-16 18:19:40,691 - directlfq.protein_intensity_estimation - INFO - lfq-object 2500\n", + "2024-01-16 18:19:41,264 - directlfq.protein_intensity_estimation - INFO - lfq-object 2800\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:49:14,326 - directlfq.protein_intensity_estimation - INFO - prot 2800\n", - "2023-12-04 19:49:14,427 - directlfq.protein_intensity_estimation - INFO - prot 500\n", - "2023-12-04 19:49:14,560 - directlfq.protein_intensity_estimation - INFO - prot 3000\n", - "2023-12-04 19:49:14,799 - directlfq.protein_intensity_estimation - INFO - prot 800\n", - "2023-12-04 19:49:15,007 - directlfq.protein_intensity_estimation - INFO - prot 1400\n", - "2023-12-04 19:49:15,041 - directlfq.protein_intensity_estimation - INFO - prot 1100\n", + "2024-01-16 18:19:42,381 - directlfq.protein_intensity_estimation - INFO - lfq-object 500\n", + "2024-01-16 18:19:42,941 - directlfq.protein_intensity_estimation - INFO - lfq-object 3000\n", + "2024-01-16 18:19:43,043 - directlfq.protein_intensity_estimation - INFO - lfq-object 800\n", + "2024-01-16 18:19:43,185 - directlfq.protein_intensity_estimation - INFO - lfq-object 1400\n", + "2024-01-16 18:19:43,321 - directlfq.protein_intensity_estimation - INFO - lfq-object 1100\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:49:15,466 - directlfq.protein_intensity_estimation - INFO - prot 1700\n", - "2023-12-04 19:49:15,630 - directlfq.protein_intensity_estimation - INFO - prot 2600\n", - "2023-12-04 19:49:15,717 - directlfq.protein_intensity_estimation - INFO - prot 2000\n", - "2023-12-04 19:49:15,771 - directlfq.protein_intensity_estimation - INFO - prot 2300\n", + "2024-01-16 18:19:43,959 - directlfq.protein_intensity_estimation - INFO - lfq-object 1700\n", + "2024-01-16 18:19:44,054 - directlfq.protein_intensity_estimation - INFO - lfq-object 2600\n", + "2024-01-16 18:19:44,564 - directlfq.protein_intensity_estimation - INFO - lfq-object 2000\n", + "2024-01-16 18:19:44,660 - directlfq.protein_intensity_estimation - INFO - lfq-object 2300\n", + "2024-01-16 18:19:45,507 - directlfq.protein_intensity_estimation - INFO - lfq-object 2900\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:49:16,594 - directlfq.protein_intensity_estimation - INFO - prot 2900\n", - "2023-12-04 19:49:16,687 - directlfq.protein_intensity_estimation - INFO - prot 3100\n", - "2023-12-04 19:49:17,010 - directlfq.protein_intensity_estimation - INFO - prot 3300\n", - "2023-12-04 19:49:17,407 - directlfq.protein_intensity_estimation - INFO - prot 3600\n", - "2023-12-04 19:49:17,747 - directlfq.protein_intensity_estimation - INFO - prot 3900\n", - "2023-12-04 19:49:18,171 - directlfq.protein_intensity_estimation - INFO - prot 4200\n", - "2023-12-04 19:49:18,341 - directlfq.protein_intensity_estimation - INFO - prot 4500\n", - "2023-12-04 19:50:23,658 - directlfq.protein_intensity_estimation - INFO - prot 4800\n", - "2023-12-04 19:50:23,899 - directlfq.protein_intensity_estimation - INFO - prot 3200\n", - "2023-12-04 19:50:23,965 - directlfq.protein_intensity_estimation - INFO - prot 5100\n", - "2023-12-04 19:50:24,056 - directlfq.protein_intensity_estimation - INFO - prot 3400\n", - "2023-12-04 19:50:24,219 - directlfq.protein_intensity_estimation - INFO - prot 3700\n", - "2023-12-04 19:50:24,231 - directlfq.protein_intensity_estimation - INFO - prot 5400\n", - "2023-12-04 19:50:24,499 - directlfq.protein_intensity_estimation - INFO - prot 5700\n", - "2023-12-04 19:50:24,876 - directlfq.protein_intensity_estimation - INFO - prot 4000\n", + "2024-01-16 18:19:46,657 - directlfq.protein_intensity_estimation - INFO - lfq-object 3100\n", + "2024-01-16 18:19:47,120 - directlfq.protein_intensity_estimation - INFO - lfq-object 3300\n", + "2024-01-16 18:19:47,595 - directlfq.protein_intensity_estimation - INFO - lfq-object 3600\n", + "2024-01-16 18:19:48,282 - directlfq.protein_intensity_estimation - INFO - lfq-object 3900\n", + "2024-01-16 18:19:48,725 - directlfq.protein_intensity_estimation - INFO - lfq-object 4200\n", + "2024-01-16 18:19:49,178 - directlfq.protein_intensity_estimation - INFO - lfq-object 4500\n", + "2024-01-16 18:19:49,475 - directlfq.protein_intensity_estimation - INFO - lfq-object 4800\n", + "2024-01-16 18:19:50,040 - directlfq.protein_intensity_estimation - INFO - lfq-object 5100\n", + "2024-01-16 18:19:50,428 - directlfq.protein_intensity_estimation - INFO - lfq-object 5400\n", + "2024-01-16 18:19:50,524 - directlfq.protein_intensity_estimation - INFO - lfq-object 3200\n", + "2024-01-16 18:19:50,575 - directlfq.protein_intensity_estimation - INFO - lfq-object 3700\n", + "2024-01-16 18:19:50,588 - directlfq.protein_intensity_estimation - INFO - lfq-object 3400\n", + "2024-01-16 18:19:50,863 - directlfq.protein_intensity_estimation - INFO - lfq-object 5700\n", + "2024-01-16 18:19:51,907 - directlfq.protein_intensity_estimation - INFO - lfq-object 4000\n", + "2024-01-16 18:19:52,018 - directlfq.protein_intensity_estimation - INFO - lfq-object 4300\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:25,057 - directlfq.protein_intensity_estimation - INFO - prot 4300\n", - "2023-12-04 19:50:25,314 - directlfq.protein_intensity_estimation - INFO - prot 4900\n", - "2023-12-04 19:50:25,811 - directlfq.protein_intensity_estimation - INFO - prot 6000\n", - "2023-12-04 19:50:25,801 - directlfq.protein_intensity_estimation - INFO - prot 4600\n", - "2023-12-04 19:50:25,971 - directlfq.protein_intensity_estimation - INFO - prot 3500\n", + "2024-01-16 18:19:52,369 - directlfq.protein_intensity_estimation - INFO - lfq-object 4900\n", + "2024-01-16 18:19:53,058 - directlfq.protein_intensity_estimation - INFO - lfq-object 4600\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:26,221 - directlfq.protein_intensity_estimation - INFO - prot 3800\n", - "2023-12-04 19:50:26,290 - directlfq.protein_intensity_estimation - INFO - prot 5500\n", + "2024-01-16 18:19:53,805 - directlfq.protein_intensity_estimation - INFO - lfq-object 3500\n", + "2024-01-16 18:19:53,866 - directlfq.protein_intensity_estimation - INFO - lfq-object 3800\n", + "2024-01-16 18:19:53,879 - directlfq.protein_intensity_estimation - INFO - lfq-object 5500\n", + "2024-01-16 18:19:53,919 - directlfq.protein_intensity_estimation - INFO - lfq-object 6000\n", + "2024-01-16 18:19:53,928 - directlfq.protein_intensity_estimation - INFO - lfq-object 5800\n", + "2024-01-16 18:19:54,052 - directlfq.protein_intensity_estimation - INFO - lfq-object 5200\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:26,370 - directlfq.protein_intensity_estimation - INFO - prot 5200\n", - "2023-12-04 19:50:26,372 - directlfq.protein_intensity_estimation - INFO - prot 5800\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:27,393 - directlfq.protein_intensity_estimation - INFO - prot 4100\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:19:55,981 - directlfq.protein_intensity_estimation - INFO - lfq-object 4100\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:27,549 - directlfq.protein_intensity_estimation - INFO - prot 4700\n", - "2023-12-04 19:50:27,734 - directlfq.protein_intensity_estimation - INFO - prot 5000\n", - "2023-12-04 19:50:27,756 - directlfq.protein_intensity_estimation - INFO - prot 4400\n", - "2023-12-04 19:50:27,905 - directlfq.protein_intensity_estimation - INFO - prot 6100\n", - "2023-12-04 19:50:27,918 - directlfq.protein_intensity_estimation - INFO - prot 5600\n", - "2023-12-04 19:50:28,071 - directlfq.protein_intensity_estimation - INFO - prot 6300\n", - "2023-12-04 19:50:28,087 - directlfq.protein_intensity_estimation - INFO - prot 5900\n", - "2023-12-04 19:50:28,473 - directlfq.protein_intensity_estimation - INFO - prot 6600\n", + "2024-01-16 18:19:56,064 - directlfq.protein_intensity_estimation - INFO - lfq-object 4700\n", + "2024-01-16 18:19:56,398 - directlfq.protein_intensity_estimation - INFO - lfq-object 5000\n", + "2024-01-16 18:19:56,676 - directlfq.protein_intensity_estimation - INFO - lfq-object 4400\n", + "2024-01-16 18:19:56,794 - directlfq.protein_intensity_estimation - INFO - lfq-object 5600\n", + "2024-01-16 18:19:57,007 - directlfq.protein_intensity_estimation - INFO - lfq-object 5900\n", + "2024-01-16 18:19:57,303 - directlfq.protein_intensity_estimation - INFO - lfq-object 6300\n", + "2024-01-16 18:19:57,801 - directlfq.protein_intensity_estimation - INFO - lfq-object 6100\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:28,662 - directlfq.protein_intensity_estimation - INFO - prot 5300\n", + "2024-01-16 18:19:57,894 - directlfq.protein_intensity_estimation - INFO - lfq-object 5300\n", + "2024-01-16 18:19:58,127 - directlfq.protein_intensity_estimation - INFO - lfq-object 6600\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:19:59,660 - directlfq.protein_intensity_estimation - INFO - lfq-object 6900\n", + "2024-01-16 18:20:00,356 - directlfq.protein_intensity_estimation - INFO - lfq-object 7200\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:29,821 - directlfq.protein_intensity_estimation - INFO - prot 6900\n", - "2023-12-04 19:50:29,843 - directlfq.protein_intensity_estimation - INFO - prot 6200\n", - "2023-12-04 19:50:30,102 - directlfq.protein_intensity_estimation - INFO - prot 7200\n", - "2023-12-04 19:50:30,389 - directlfq.protein_intensity_estimation - INFO - prot 7500\n", - "2023-12-04 19:50:30,697 - directlfq.protein_intensity_estimation - INFO - prot 7800\n", - "2023-12-04 19:50:30,735 - directlfq.protein_intensity_estimation - INFO - prot 6400\n", - "2023-12-04 19:50:31,005 - directlfq.protein_intensity_estimation - INFO - prot 8100\n", - "2023-12-04 19:50:31,219 - directlfq.protein_intensity_estimation - INFO - prot 6700\n", - "2023-12-04 19:50:31,380 - directlfq.protein_intensity_estimation - INFO - prot 8400\n", - "2023-12-04 19:50:31,826 - directlfq.protein_intensity_estimation - INFO - prot 8700\n", - "2023-12-04 19:50:31,921 - directlfq.protein_intensity_estimation - INFO - prot 7000\n", - "2023-12-04 19:50:32,103 - directlfq.protein_intensity_estimation - INFO - prot 9000\n", - "2023-12-04 19:50:32,394 - directlfq.protein_intensity_estimation - INFO - prot 7300\n", - "2023-12-04 19:50:32,504 - directlfq.protein_intensity_estimation - INFO - prot 7600\n", + "2024-01-16 18:20:00,856 - directlfq.protein_intensity_estimation - INFO - lfq-object 7500\n", + "2024-01-16 18:20:00,891 - directlfq.protein_intensity_estimation - INFO - lfq-object 6200\n", + "2024-01-16 18:20:01,329 - directlfq.protein_intensity_estimation - INFO - lfq-object 7800\n", + "2024-01-16 18:20:01,969 - directlfq.protein_intensity_estimation - INFO - lfq-object 8100\n", + "2024-01-16 18:20:02,341 - directlfq.protein_intensity_estimation - INFO - lfq-object 6400\n", + "2024-01-16 18:20:02,961 - directlfq.protein_intensity_estimation - INFO - lfq-object 8400\n", + "2024-01-16 18:20:02,960 - directlfq.protein_intensity_estimation - INFO - lfq-object 8700\n", + "2024-01-16 18:20:03,644 - directlfq.protein_intensity_estimation - INFO - lfq-object 6700\n", + "2024-01-16 18:20:04,057 - directlfq.protein_intensity_estimation - INFO - lfq-object 7000\n", + "2024-01-16 18:20:04,106 - directlfq.protein_intensity_estimation - INFO - lfq-object 9000\n", + "2024-01-16 18:20:04,884 - directlfq.protein_intensity_estimation - INFO - lfq-object 7300\n", + "2024-01-16 18:20:05,231 - directlfq.protein_intensity_estimation - INFO - lfq-object 7600\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:33,035 - directlfq.protein_intensity_estimation - INFO - prot 7900\n", + "2024-01-16 18:20:06,163 - directlfq.protein_intensity_estimation - INFO - lfq-object 7900\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:33,306 - directlfq.protein_intensity_estimation - INFO - prot 8200\n", - "2023-12-04 19:50:33,345 - directlfq.protein_intensity_estimation - INFO - prot 6500\n", - "2023-12-04 19:50:33,365 - directlfq.protein_intensity_estimation - INFO - prot 8500\n", - "2023-12-04 19:50:33,805 - directlfq.protein_intensity_estimation - INFO - prot 7100\n", - "2023-12-04 19:50:33,872 - directlfq.protein_intensity_estimation - INFO - prot 6800\n", + "2024-01-16 18:20:06,588 - directlfq.protein_intensity_estimation - INFO - lfq-object 8200\n", + "2024-01-16 18:20:06,596 - directlfq.protein_intensity_estimation - INFO - lfq-object 8500\n", + "2024-01-16 18:20:07,105 - directlfq.protein_intensity_estimation - INFO - lfq-object 6500\n", + "2024-01-16 18:20:07,322 - directlfq.protein_intensity_estimation - INFO - lfq-object 7100\n", + "2024-01-16 18:20:07,374 - directlfq.protein_intensity_estimation - INFO - lfq-object 8800\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:34,201 - directlfq.protein_intensity_estimation - INFO - prot 8800\n", + "2024-01-16 18:20:08,203 - directlfq.protein_intensity_estimation - INFO - lfq-object 9100\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:34,475 - directlfq.protein_intensity_estimation - INFO - prot 9100\n", - "2023-12-04 19:50:34,810 - directlfq.protein_intensity_estimation - INFO - prot 7400\n", - "2023-12-04 19:50:34,834 - directlfq.protein_intensity_estimation - INFO - prot 7700\n", + "2024-01-16 18:20:08,658 - directlfq.protein_intensity_estimation - INFO - lfq-object 6800\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:35,748 - directlfq.protein_intensity_estimation - INFO - prot 8000\n", - "2023-12-04 19:50:36,095 - directlfq.protein_intensity_estimation - INFO - prot 8600\n", - "2023-12-04 19:50:36,237 - directlfq.protein_intensity_estimation - INFO - prot 8300\n", + "2024-01-16 18:20:08,981 - directlfq.protein_intensity_estimation - INFO - lfq-object 7400\n", + "2024-01-16 18:20:09,036 - directlfq.protein_intensity_estimation - INFO - lfq-object 7700\n", + "2024-01-16 18:20:10,196 - directlfq.protein_intensity_estimation - INFO - lfq-object 8000\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:36,579 - directlfq.protein_intensity_estimation - INFO - prot 9300\n", + "2024-01-16 18:20:10,546 - directlfq.protein_intensity_estimation - INFO - lfq-object 8300\n", + "2024-01-16 18:20:10,697 - directlfq.protein_intensity_estimation - INFO - lfq-object 8600\n", + "2024-01-16 18:20:11,157 - directlfq.protein_intensity_estimation - INFO - lfq-object 9300\n", + "2024-01-16 18:20:11,507 - directlfq.protein_intensity_estimation - INFO - lfq-object 8900\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", + "2024-01-16 18:20:11,989 - directlfq.protein_intensity_estimation - INFO - lfq-object 9200\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:37,042 - directlfq.protein_intensity_estimation - INFO - prot 9600\n", - "2023-12-04 19:50:37,094 - directlfq.protein_intensity_estimation - INFO - prot 8900\n", - "2023-12-04 19:50:37,273 - directlfq.protein_intensity_estimation - INFO - prot 9200\n", - "2023-12-04 19:50:37,342 - directlfq.protein_intensity_estimation - INFO - prot 9900\n", - "2023-12-04 19:50:37,679 - directlfq.protein_intensity_estimation - INFO - prot 10200\n", - "2023-12-04 19:50:38,049 - directlfq.protein_intensity_estimation - INFO - prot 10500\n", + "2024-01-16 18:20:12,901 - directlfq.protein_intensity_estimation - INFO - lfq-object 9600\n", + "2024-01-16 18:20:13,514 - directlfq.protein_intensity_estimation - INFO - lfq-object 9900\n", + "2024-01-16 18:20:14,489 - directlfq.protein_intensity_estimation - INFO - lfq-object 10200\n", + "2024-01-16 18:20:14,769 - directlfq.protein_intensity_estimation - INFO - lfq-object 9400\n", + "2024-01-16 18:20:14,834 - directlfq.protein_intensity_estimation - INFO - lfq-object 10500\n", + "2024-01-16 18:20:15,269 - directlfq.protein_intensity_estimation - INFO - lfq-object 10800\n", + "2024-01-16 18:20:15,685 - directlfq.protein_intensity_estimation - INFO - lfq-object 11100\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:38,523 - directlfq.protein_intensity_estimation - INFO - prot 10800\n", - "2023-12-04 19:50:38,707 - directlfq.protein_intensity_estimation - INFO - prot 9400\n", - "2023-12-04 19:50:39,169 - directlfq.protein_intensity_estimation - INFO - prot 11100\n", - "2023-12-04 19:50:39,344 - directlfq.protein_intensity_estimation - INFO - prot 9700\n", - "2023-12-04 19:50:39,377 - directlfq.protein_intensity_estimation - INFO - prot 10000\n", - "2023-12-04 19:50:39,504 - directlfq.protein_intensity_estimation - INFO - prot 11400\n", - "2023-12-04 19:50:39,944 - directlfq.protein_intensity_estimation - INFO - prot 10300\n", - "2023-12-04 19:50:40,032 - directlfq.protein_intensity_estimation - INFO - prot 11700\n", - "2023-12-04 19:50:40,227 - directlfq.protein_intensity_estimation - INFO - prot 10600\n", - "2023-12-04 19:50:40,791 - directlfq.protein_intensity_estimation - INFO - prot 9500\n", - "2023-12-04 19:50:40,862 - directlfq.protein_intensity_estimation - INFO - prot 10900\n", - "2023-12-04 19:50:41,283 - directlfq.protein_intensity_estimation - INFO - prot 11200\n", - "2023-12-04 19:50:41,509 - directlfq.protein_intensity_estimation - INFO - prot 9800\n", - "2023-12-04 19:50:41,587 - directlfq.protein_intensity_estimation - INFO - prot 10100\n", + "2024-01-16 18:20:16,151 - directlfq.protein_intensity_estimation - INFO - lfq-object 11400\n", + "2024-01-16 18:20:16,677 - directlfq.protein_intensity_estimation - INFO - lfq-object 9700\n", + "2024-01-16 18:20:16,825 - directlfq.protein_intensity_estimation - INFO - lfq-object 10000\n", + "2024-01-16 18:20:17,014 - directlfq.protein_intensity_estimation - INFO - lfq-object 11700\n", + "2024-01-16 18:20:18,122 - directlfq.protein_intensity_estimation - INFO - lfq-object 10300\n", + "2024-01-16 18:20:18,338 - directlfq.protein_intensity_estimation - INFO - lfq-object 9500\n", + "2024-01-16 18:20:18,413 - directlfq.protein_intensity_estimation - INFO - lfq-object 10600\n", + "2024-01-16 18:20:19,311 - directlfq.protein_intensity_estimation - INFO - lfq-object 10900\n", + "2024-01-16 18:20:19,362 - directlfq.protein_intensity_estimation - INFO - lfq-object 11200\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:41,770 - directlfq.protein_intensity_estimation - INFO - prot 11500\n", + "2024-01-16 18:20:19,982 - directlfq.protein_intensity_estimation - INFO - lfq-object 11500\n", + "2024-01-16 18:20:20,320 - directlfq.protein_intensity_estimation - INFO - lfq-object 9800\n", + "2024-01-16 18:20:20,584 - directlfq.protein_intensity_estimation - INFO - lfq-object 10100\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:42,161 - directlfq.protein_intensity_estimation - INFO - prot 10400\n", - "2023-12-04 19:50:42,361 - directlfq.protein_intensity_estimation - INFO - prot 10700\n", - "2023-12-04 19:50:42,415 - directlfq.protein_intensity_estimation - INFO - prot 11800\n", - "2023-12-04 19:50:42,958 - directlfq.protein_intensity_estimation - INFO - prot 11000\n", - "2023-12-04 19:50:43,553 - directlfq.protein_intensity_estimation - INFO - prot 11300\n", + "2024-01-16 18:20:21,224 - directlfq.protein_intensity_estimation - INFO - lfq-object 11800\n", + "2024-01-16 18:20:21,917 - directlfq.protein_intensity_estimation - INFO - lfq-object 10400\n", + "2024-01-16 18:20:21,952 - directlfq.protein_intensity_estimation - INFO - lfq-object 10700\n", + "2024-01-16 18:20:22,755 - directlfq.protein_intensity_estimation - INFO - lfq-object 11000\n", + "2024-01-16 18:20:23,267 - directlfq.protein_intensity_estimation - INFO - lfq-object 11300\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/numpy/lib/nanfunctions.py:1217: RuntimeWarning: All-NaN slice encountered\n", " r, k = function_base._ureduce(a, func=_nanmedian, axis=axis, out=out,\n", - "2023-12-04 19:50:44,156 - directlfq.protein_intensity_estimation - INFO - prot 11600\n", - "2023-12-04 19:50:44,438 - directlfq.protein_intensity_estimation - INFO - prot 11900\n", - "2023-12-04 19:51:01,052 - directlfq.lfq_manager - INFO - Writing results files.\n", - "2023-12-04 19:52:13,294 - directlfq.lfq_manager - INFO - Analysis finished!\n" + "2024-01-16 18:20:24,026 - directlfq.protein_intensity_estimation - INFO - lfq-object 11600\n", + "2024-01-16 18:20:24,778 - directlfq.protein_intensity_estimation - INFO - lfq-object 11900\n", + "2024-01-16 18:20:33,322 - directlfq.lfq_manager - INFO - Writing results files.\n", + "2024-01-16 18:20:42,481 - directlfq.lfq_manager - INFO - Analysis finished!\n" ] } ], @@ -677,7 +681,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 6, "metadata": {}, "outputs": [ { @@ -728,7 +732,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 7, "metadata": {}, "outputs": [ { @@ -1410,7 +1414,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -1421,7 +1425,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 9, "metadata": {}, "outputs": [], "source": [ @@ -1436,7 +1440,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -1515,7 +1519,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 11, "metadata": {}, "outputs": [ { @@ -1904,7 +1908,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 12, "metadata": {}, "outputs": [ { @@ -1930,11 +1934,6 @@ "YEAST num:3097 median_FC:1.4 STD:0.32\n", "\n", "HUMAN num:8571 median_FC:-0.024 STD:0.1\n", - "\n", - "directLFQ (fragions top3)\n", - "YEAST num:3097 median_FC:1.5 STD:0.32\n", - "\n", - "HUMAN num:8571 median_FC:-0.027 STD:0.099\n", "\n" ] }, @@ -1949,7 +1948,24 @@ "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/pandas/core/arraylike.py:402: RuntimeWarning: divide by zero encountered in log2\n", " result = getattr(ufunc, method)(*inputs, **kwargs)\n", "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/pandas/core/arraylike.py:402: RuntimeWarning: divide by zero encountered in log2\n", - " result = getattr(ufunc, method)(*inputs, **kwargs)\n", + " result = getattr(ufunc, method)(*inputs, **kwargs)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "directLFQ (fragions top3)\n", + "YEAST num:3097 median_FC:1.5 STD:0.32\n", + "\n", + "HUMAN num:8571 median_FC:-0.027 STD:0.099\n", + "\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ "/Users/constantin/opt/anaconda3/envs/directlfq/lib/python3.8/site-packages/pandas/core/arraylike.py:402: RuntimeWarning: divide by zero encountered in log2\n", " result = getattr(ufunc, method)(*inputs, **kwargs)\n" ] @@ -1957,10 +1973,10 @@ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 20, + "execution_count": 12, "metadata": {}, "output_type": "execute_result" }, @@ -2041,7 +2057,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 13, "metadata": {}, "outputs": [ { @@ -2051,7 +2067,7 @@ "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", - "\u001b[1;32m/Users/constantin/workspace/directlfq/tests/ratio_tests/compare_diapasef_diann.ipynb Cell 14\u001b[0m line \u001b[0;36m2\n\u001b[1;32m 1\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mpandas\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mpd\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m diann_df \u001b[39m=\u001b[39m pd\u001b[39m.\u001b[39mread_csv(input_file, sep\u001b[39m=\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m\\t\u001b[39;00m\u001b[39m\"\u001b[39m)\n", + "Cell \u001b[0;32mIn[13], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mpandas\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mpd\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m diann_df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mread_csv(\u001b[43minput_file\u001b[49m, sep\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;130;01m\\t\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n", "\u001b[0;31mNameError\u001b[0m: name 'input_file' is not defined" ] } From 9c7859793cb035883b16ee502475459221f74074 Mon Sep 17 00:00:00 2001 From: ammarcsj <70114795+ammarcsj@users.noreply.github.com> Date: Tue, 16 Jan 2024 18:47:49 +0100 Subject: [PATCH 6/8] clean nb --- .../03_protein_intensity_estimation.ipynb | 38 +++++++------------ 1 file changed, 13 insertions(+), 25 deletions(-) diff --git a/nbdev_nbs/03_protein_intensity_estimation.ipynb b/nbdev_nbs/03_protein_intensity_estimation.ipynb index c0e6c97..8dc0b48 100644 --- a/nbdev_nbs/03_protein_intensity_estimation.ipynb +++ b/nbdev_nbs/03_protein_intensity_estimation.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -11,7 +11,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -47,7 +47,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -97,7 +97,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -944,7 +944,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -1090,7 +1090,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -1305,7 +1305,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1340,7 +1340,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1361,7 +1361,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -1435,7 +1435,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1451,7 +1451,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -1529,7 +1529,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1544,7 +1544,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -1582,18 +1582,6 @@ "display_name": "alphatemplate", "language": "python", "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.8.17" } }, "nbformat": 4, From 6abbe2ebcb288529ba7e104d9c04c09e58ea0057 Mon Sep 17 00:00:00 2001 From: ammarcsj <70114795+ammarcsj@users.noreply.github.com> Date: Tue, 16 Jan 2024 18:48:01 +0100 Subject: [PATCH 7/8] =?UTF-8?q?Bump=20version:=200.2.15=20=E2=86=92=200.2.?= =?UTF-8?q?16?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- directlfq/__init__.py | 2 +- misc/bumpversion.cfg | 2 +- release/one_click_linux_gui/control | 2 +- release/one_click_linux_gui/create_installer_linux.sh | 2 +- release/one_click_macos_gui/Info.plist | 4 ++-- release/one_click_macos_gui/create_installer_macos.sh | 4 ++-- release/one_click_macos_gui/distribution.xml | 2 +- release/one_click_windows_gui/create_installer_windows.sh | 2 +- release/one_click_windows_gui/directlfq_innoinstaller.iss | 2 +- settings.ini | 2 +- 10 files changed, 12 insertions(+), 12 deletions(-) diff --git a/directlfq/__init__.py b/directlfq/__init__.py index 10aac85..568bfb3 100644 --- a/directlfq/__init__.py +++ b/directlfq/__init__.py @@ -2,7 +2,7 @@ __project__ = "directlfq" -__version__ = "0.2.15" +__version__ = "0.2.16" __license__ = "Apache" __description__ = "An open-source Python package of the AlphaPept ecosystem" __author__ = "Mann Labs" diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg index 83d3bdb..4c54d50 100644 --- a/misc/bumpversion.cfg +++ b/misc/bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.2.15 +current_version = 0.2.16 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/release/one_click_linux_gui/control b/release/one_click_linux_gui/control index 63ee781..766e804 100644 --- a/release/one_click_linux_gui/control +++ b/release/one_click_linux_gui/control @@ -1,5 +1,5 @@ Package: directlfq -Version: 0.2.15 +Version: 0.2.16 Architecture: all Maintainer: Mann Labs Description: directlfq diff --git a/release/one_click_linux_gui/create_installer_linux.sh b/release/one_click_linux_gui/create_installer_linux.sh index 7b08de0..3867aa0 100644 --- a/release/one_click_linux_gui/create_installer_linux.sh +++ b/release/one_click_linux_gui/create_installer_linux.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_linux_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/directlfq-0.2.15-py3-none-any.whl[stable, gui]" +pip install "../../dist/directlfq-0.2.16-py3-none-any.whl[stable, gui]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.10 diff --git a/release/one_click_macos_gui/Info.plist b/release/one_click_macos_gui/Info.plist index f896f3c..dd912ba 100644 --- a/release/one_click_macos_gui/Info.plist +++ b/release/one_click_macos_gui/Info.plist @@ -9,9 +9,9 @@ CFBundleIconFile alpha_logo.icns CFBundleIdentifier - directlfq.0.2.15 + directlfq.0.2.16 CFBundleShortVersionString - 0.2.15 + 0.2.16 CFBundleInfoDictionaryVersion 6.0 CFBundleName diff --git a/release/one_click_macos_gui/create_installer_macos.sh b/release/one_click_macos_gui/create_installer_macos.sh index 8e7d90a..843455d 100755 --- a/release/one_click_macos_gui/create_installer_macos.sh +++ b/release/one_click_macos_gui/create_installer_macos.sh @@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_macos_gui -pip install "../../dist/directlfq-0.2.15-py3-none-any.whl[stable, gui]" +pip install "../../dist/directlfq-0.2.16-py3-none-any.whl[stable, gui]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.10 @@ -40,5 +40,5 @@ cp ../../LICENSE Resources/LICENSE cp ../logos/alpha_logo.png Resources/alpha_logo.png chmod 777 scripts/* -pkgbuild --root dist/directlfq --identifier de.mpg.biochem.directlfq.app --version 0.2.15 --install-location /Applications/directlfq.app --scripts scripts directlfq.pkg +pkgbuild --root dist/directlfq --identifier de.mpg.biochem.directlfq.app --version 0.2.16 --install-location /Applications/directlfq.app --scripts scripts directlfq.pkg productbuild --distribution distribution.xml --resources Resources --package-path directlfq.pkg dist/directlfq_gui_installer_macos.pkg diff --git a/release/one_click_macos_gui/distribution.xml b/release/one_click_macos_gui/distribution.xml index a9a6c0f..0a2f3cc 100644 --- a/release/one_click_macos_gui/distribution.xml +++ b/release/one_click_macos_gui/distribution.xml @@ -1,6 +1,6 @@ - directlfq 0.2.15 + directlfq 0.2.16 diff --git a/release/one_click_windows_gui/create_installer_windows.sh b/release/one_click_windows_gui/create_installer_windows.sh index 15d435c..1e09c04 100644 --- a/release/one_click_windows_gui/create_installer_windows.sh +++ b/release/one_click_windows_gui/create_installer_windows.sh @@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel # Setting up the local package cd release/one_click_windows_gui # Make sure you include the required extra packages and always use the stable or very-stable options! -pip install "../../dist/directlfq-0.2.15-py3-none-any.whl[stable, gui]" +pip install "../../dist/directlfq-0.2.16-py3-none-any.whl[stable, gui]" # Creating the stand-alone pyinstaller folder pip install pyinstaller==4.10 diff --git a/release/one_click_windows_gui/directlfq_innoinstaller.iss b/release/one_click_windows_gui/directlfq_innoinstaller.iss index 7705c22..fd63e7b 100644 --- a/release/one_click_windows_gui/directlfq_innoinstaller.iss +++ b/release/one_click_windows_gui/directlfq_innoinstaller.iss @@ -2,7 +2,7 @@ ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES! #define MyAppName "directlfq" -#define MyAppVersion "0.2.15" +#define MyAppVersion "0.2.16" #define MyAppPublisher "Max Planck Institute of Biochemistry and the University of Copenhagen, Mann Labs" #define MyAppURL "https://github.com/MannLabs/directlfq" #define MyAppExeName "directlfq_gui.exe" diff --git a/settings.ini b/settings.ini index b45ffad..8e15b8e 100644 --- a/settings.ini +++ b/settings.ini @@ -13,7 +13,7 @@ author = Constantin Ammar author_email = constantin.ammar@gmail.com copyright = fast.ai branch = master -version = 0.2.15 +version = 0.2.16 min_python = 3.6 audience = Developers language = English From 07c24163a2c21ff41bfaaeaf6ef1b14d9c80267c Mon Sep 17 00:00:00 2001 From: ammarcsj <70114795+ammarcsj@users.noreply.github.com> Date: Tue, 16 Jan 2024 19:19:25 +0100 Subject: [PATCH 8/8] remove redundant cell w. display command --- ...n_pipeline_w_different_input_formats.ipynb | 36 ------------------- 1 file changed, 36 deletions(-) diff --git a/tests/quicktests/run_pipeline_w_different_input_formats.ipynb b/tests/quicktests/run_pipeline_w_different_input_formats.ipynb index 3d381d8..3c30641 100644 --- a/tests/quicktests/run_pipeline_w_different_input_formats.ipynb +++ b/tests/quicktests/run_pipeline_w_different_input_formats.ipynb @@ -206,42 +206,6 @@ " lfq_manager.run_lfq(spectronaut_quicktest_file, selected_proteins_file=spectronaut_protein_subset, num_cores=1, compile_normalized_ion_table=True)\n", " lfq_manager.run_lfq(spectronaut_quicktest_file)" ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "array([[1, 4],\n", - " [2, 5],\n", - " [3, 6]])" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "import pandas as pd\n", - "\n", - "# Sample dataframe\n", - "df = pd.DataFrame({'A': [1, 2, 3], 'B': [4, 5, 6]}, index=['x', 'y', 'z'])\n", - "\n", - "# Convert to NumPy array\n", - "array = df.to_numpy()\n", - "\n", - "display(array)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": {