Prep_formated_sequence_data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "hazardous-mauritius",
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "import os\n",
    "from pyteomics import fasta\n",
    "import pandas as pd\n",
    "import alphamap\n",
    "from alphamap.importing import import_data\n",
    "from alphamap.preprocessing import format_input_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "average-lotus",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Import MaxQuant output\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q2UVX4 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q3ZAW8 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02533 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P13645 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02538 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P04259 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P48668 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P04264 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02769 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for  in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q3SX28 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q28107 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q3SX14 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P81644 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for REFSEQ:XP_092267 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P19012 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P08779 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for ENSEMBL:ENSP00000377550 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P13646-1 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q04695 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02535-1 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q3MHH8 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for ENSEMBL:ENSBTAP00000001528 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P15636 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P00761 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P35908v2 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P35908 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q28194 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P13647 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for ENSEMBL:ENSBTAP00000038253 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P17690 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P01966 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q3ZBD7 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for ENSEMBL:ENSBTAP00000025008 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P62894 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P67983 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02676 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P12763 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02584 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q148H6 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q7Z3Y7 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q7Z3Z0 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q7Z3Y8 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02672 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P35527 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for ENSEMBL:ENSBTAP00000031900 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02662 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q29443 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q0IIK2 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02666 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q9H552 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P07224 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02663 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P21752 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P41361 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q7Z794 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q3KNV1 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P08729 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q61726 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q6NT21 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P78385 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q5D862 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for ENSEMBL:ENSBTAP00000007350 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P04258 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q86YZ3 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P34955 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q9TRI1 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P01030 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q95121 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q2M2I5 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for A2A5Y0 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for O76013 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for REFSEQ:XP_986630 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for O76015 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for A2AB72 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for O76014 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q14532 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q92764 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q9UE12 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q15323 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for A2A4G1 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for REFSEQ:XP_932229 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q3SX09 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q61782 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P02070 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for H-INV:HIT000016045 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P06868 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P35900 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for P15497 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n",
      "C:\\Users\\fhansen\\AppData\\Local\\Continuum\\envs\\Mito_eLife\\lib\\site-packages\\alphamap\\preprocessing.py:65: UserWarning: No matching entry for Q7Z3Y9 in the selected fasta.\n",
      "  warnings.warn(f'No matching entry for {prot} in the selected fasta.')\n"
     ]
    }
   ],
   "source": [
    "path = os.path.dirname(os.path.abspath('__file__'))+'\\\\MQ_Output\\\\'\n",
    "full_proteome_data = import_data(path+'evidence.txt')\n",
    "\n",
    "path_fasta = os.path.dirname(os.path.abspath('__file__'))\n",
    "full_mouse_fasta = fasta.IndexedUniProt(path_fasta+'\\\\20201019_Mus musculus_10090_UP000000589.fasta')\n",
    "\n",
    "formatted_proteome_data = format_input_data(df=full_proteome_data, fasta = full_mouse_fasta, modification_exp = r'\\[.*?\\]')\n",
    "\n",
    "path_saving = os.path.dirname(os.path.abspath('__file__'))+'\\\\Prepared_tables\\\\'\n",
    "formatted_proteome_data.to_csv((path_saving+ 'formatted_proteome_data.csv'), index= False)"
   ]
  }
 ],
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