correct bugs

sky1ove · Sep 27, 2024 · f4de050 · f4de050
1 parent e2dc27e
commit f4de050
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Showing 7 changed files with 28 additions and 17 deletions.
diff --git a/katlas_raw/__init__.py b/katlas_raw/__init__.py
@@ -0,0 +1 @@
+__version__ = "0.0.1"
diff --git a/katlas_raw/_modidx.py b/katlas_raw/_modidx.py
@@ -0,0 +1,8 @@
+# Autogenerated by nbdev
+
+d = { 'settings': { 'branch': 'main',
+                'doc_baseurl': '/katlas_raw',
+                'doc_host': 'https://sky1ove.github.io',
+                'git_url': 'https://github.com/sky1ove/katlas_raw',
+                'lib_path': 'katlas_raw'},
+  'syms': {}}
diff --git a/nbs/04a_Plot_heatmap_logo_CDDM.ipynb b/nbs/04a_Plot_heatmap_logo_CDDM.ipynb
@@ -608,7 +608,7 @@
    "outputs": [],
    "source": [
     "# data.to_parquet('ks_main_upper.parquet')\n",
-    "data.to_csv('supp/CDDM_upper.csv')"
+    "# data.to_csv('supp/CDDM_upper.csv')"
    ]
   },
   {

diff --git a/nbs/07a_Combine_psp_ochoa.ipynb b/nbs/07a_Combine_psp_ochoa.ipynb
@@ -440,22 +440,14 @@
     "psp = psp[psp.LT_LIT.notna()].reset_index(drop=True)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "299536e3-8b80-4796-95ed-8fff549f0cf4",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": 23,
    "id": "6aa7326c-17b0-498d-af51-44eb4c5f66aa",
    "metadata": {},
    "outputs": [],
    "source": [
-    "psp = psp[['uniprot','site']] #'protein','gene'"
+    "psp = psp[['uniprot','site']].copy() #'protein','gene'"
    ]
   },
   {
@@ -483,7 +475,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ochoa = ochoa[['uniprot','site']]"
+    "ochoa = ochoa[['uniprot','site']].copy()"
    ]
   },
   {

diff --git a/nbs/07b_Plot_distribution.ipynb b/nbs/07b_Plot_distribution.ipynb
@@ -62,7 +62,17 @@
    "outputs": [],
    "source": [
     "# you can also directly load through Data\n",
-    "unique= Data.get_combine_site_psp_ochoa()"
+    "comb= Data.get_combine_site_psp_ochoa()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a7322a50-b68f-4ecc-85b4-5a332a09c618",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "comb['acceptor'] = comb.site_seq.str[7]"
    ]
   },
   {
@@ -72,9 +82,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "results = predict_kinase_df(unique,'site_seq',**param_CDDM_upper)\n",
+    "results = predict_kinase_df(comb,'site_seq',**param_CDDM_upper)\n",
     "\n",
-    "df = pd.concat([unique,results],axis=1)"
+    "df = pd.concat([comb,results],axis=1)"
    ]
   },
   {

diff --git a/nbs/09c_ML_analysis.ipynb b/nbs/09c_ML_analysis.ipynb
@@ -60,7 +60,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "oof_results = load_pickle('raw/oof.pkl')"
+    "oof_results = pd.read_pickle('raw/oof.pkl')"
    ]
   },
   {

diff --git a/nbs/others_02_CPTAC_IDmapping.ipynb b/nbs/others_02_CPTAC_IDmapping.ipynb
@@ -314,8 +314,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "linkedomics.to_parquet('linkedomics_ID.parquet')\n",
-    "linkedomicsKB.to_parquet('linkedomicsKB_ID.parquet')"
+    "# linkedomics.to_parquet('linkedomics_ID.parquet')\n",
+    "# linkedomicsKB.to_parquet('linkedomicsKB_ID.parquet')"
    ]
   },
   {