CHORE clean nbs

MannLabs · Sep 1, 2021 · dc5e3bd · dc5e3bd
1 parent 611eb39
commit dc5e3bd
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Showing 3 changed files with 55 additions and 69 deletions.
diff --git a/Workflow.ipynb b/Workflow.ipynb
@@ -23,7 +23,7 @@
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+   "execution_count": null,
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@@ -32,7 +32,7 @@
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@@ -48,7 +48,7 @@
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+   "execution_count": null,
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@@ -57,7 +57,7 @@
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+   "execution_count": null,
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@@ -82,7 +82,7 @@
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@@ -91,7 +91,7 @@
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+   "execution_count": null,
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@@ -115,7 +115,7 @@
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+   "execution_count": null,
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@@ -124,7 +124,7 @@
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+   "execution_count": null,
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@@ -140,7 +140,7 @@
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+   "execution_count": null,
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@@ -150,7 +150,7 @@
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@@ -7638,7 +7638,7 @@
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@@ -7657,7 +7657,7 @@
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@@ -7667,7 +7667,7 @@
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+   "execution_count": null,
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@@ -15730,7 +15730,7 @@
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+   "execution_count": null,
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@@ -15747,7 +15747,7 @@
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@@ -15756,7 +15756,7 @@
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+   "execution_count": null,
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@@ -20473,7 +20473,7 @@
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+   "execution_count": null,
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@@ -20490,7 +20490,7 @@
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-   "execution_count": 18,
+   "execution_count": null,
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@@ -20499,7 +20499,7 @@
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+   "execution_count": null,
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@@ -25976,7 +25976,7 @@
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+   "execution_count": null,
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@@ -25993,7 +25993,7 @@
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+   "execution_count": null,
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@@ -26002,10 +26002,8 @@
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-   "execution_count": 22,
-   "metadata": {
-    "scrolled": false
-   },
+   "execution_count": null,
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -29382,7 +29380,7 @@
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-   "execution_count": 23,
+   "execution_count": null,
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@@ -29399,7 +29397,7 @@
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-   "execution_count": 24,
+   "execution_count": null,
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@@ -29408,7 +29406,7 @@
   },
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-   "execution_count": 25,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -36705,18 +36703,6 @@
    "display_name": "Python 3",
    "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": "3.8.0"
   }
  },
  "nbformat": 4,

diff --git a/alphamap/_nbdev.py b/alphamap/_nbdev.py
@@ -13,17 +13,12 @@
          "convert_fragpipe_mq_mod": "Importing.ipynb",
          "import_fragpipe_data": "Importing.ipynb",
          "import_data": "Importing.ipynb",
-         "all_organisms": "organisms_data.ipynb",
-         "import_fasta": "organisms_data.ipynb",
-         "import_uniprot_annotation": "organisms_data.ipynb",
          "expand_protein_ids": "Preprocessing.ipynb",
          "pep_position_helper": "Preprocessing.ipynb",
          "get_peptide_position": "Preprocessing.ipynb",
          "get_ptm_sites": "Preprocessing.ipynb",
          "get_modifications": "Preprocessing.ipynb",
          "format_input_data": "Preprocessing.ipynb",
-         "protease_dict": "proteolytic_cleavage.ipynb",
-         "get_cleavage_sites": "proteolytic_cleavage.ipynb",
          "format_uniprot_annotation": "SequencePlot.ipynb",
          "ptm_shape_dict": "SequencePlot.ipynb",
          "get_plot_data": "SequencePlot.ipynb",
@@ -38,14 +33,19 @@
          "resolve_unclear_position": "Uniprot_integration.ipynb",
          "extract_positions": "Uniprot_integration.ipynb",
          "preprocess_uniprot": "Uniprot_integration.ipynb",
-         "uniprot_feature_dict": "Uniprot_integration.ipynb"}
+         "uniprot_feature_dict": "Uniprot_integration.ipynb",
+         "all_organisms": "organisms_data.ipynb",
+         "import_fasta": "organisms_data.ipynb",
+         "import_uniprot_annotation": "organisms_data.ipynb",
+         "protease_dict": "proteolytic_cleavage.ipynb",
+         "get_cleavage_sites": "proteolytic_cleavage.ipynb"}
 
 modules = ["importing.py",
-           "organisms_data.py",
            "preprocessing.py",
-           "proteolytic_cleavage.py",
            "sequenceplot.py",
-           "uniprot_integration.py"]
+           "uniprot_integration.py",
+           "organisms_data.py",
+           "proteolytic_cleavage.py"]
 
 doc_url = "https://mannlabs.github.io/alphamap/"