geney 1.3.75__py2.py3-none-any.whl → 1.3.77__py2.py3-none-any.whl

geney/oncosplice.py

@@ -284,15 +284,21 @@ def summarize_missplicing_event(pes, pir, es, ne, ir):
         return '-'
 
 def missense_effect(r, v):
-    if len(r.protein) != len(v.protein):
-        return '', ''
-
-    for i, (x, y) in enumerate(zip(r.protein, v.protein)):
-        if x != y:
-            aa_change = f'{x}>{y}'
-            codon_change = f'{r.orf[i*3:i*3+3]}>{v.orf[i*3:i*3+3]}'
-            return aa_change, codon_change
-    return '', ''
+    nt_changes, aa_changes = '', ''
+    if len(r.protein) != len(v.protein) or len(r.orf) != len(v.orf):
+        return '', '', -1
+
+    if r.protein != v.protein:
+        for i, (x, y) in enumerate(zip(r.protein, v.protein)):
+            if x != y:
+                aa_changes += f'{x}{i}{y},'
+
+    if r.orf.seq != v.orf.seq:
+        for i in range(len(r.protein)):
+            p = i*3
+            if r.orf.seq[p:p+3] != v.orf.seq[p:p+3]:
+                nt_changes += f'{r.orf.seq[p:p+3]}{p}{v.orf.seq[p:p+3]},'
+    return aa_changes, nt_changes
 
 # Annotating
 def OncospliceAnnotator(reference_transcript, variant_transcript, mut, ref_attributes=[], var_attributes=[]):
@@ -312,9 +318,10 @@ def OncospliceAnnotator(reference_transcript, variant_transcript, mut, ref_attri
     report['affected_intron'] = affected_intron
     report['mutation_distance_from_5'] = distance_from_5
     report['mutation_distance_from_3'] = distance_from_3
-    aa_c, c_c = missense_effect(reference_transcript, variant_transcript)
+    aa_c, c_c, pos = missense_effect(reference_transcript, variant_transcript)
     report['missense_effect'] = aa_c
     report['codon_change'] = c_c
+    report['missense_position'] = pos
     return report
 
 
@@ -435,8 +442,8 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, primary_tran
     return pd.DataFrame(results)[
         ['mut_id', 'transcript_id', 'isoform_id', 'primary_transcript', 'missplicing', 'full_missplicing',
          'exon_changes', 'splicing_codes', 'affected_exon', 'affected_intron', 'mutation_distance_from_5',
-         'mutation_distance_from_3', 'missense_effect', 'codon_change', 'reference_resemblance', 'oncosplice_score', 'percentile',
-         'isoform_prevalence', 'reference_protein', 'variant_protein', 'splicing_engine']]
+         'mutation_distance_from_3', 'missense_effect', 'codon_change', 'missense_position', 'reference_resemblance',
+         'oncosplice_score', 'percentile', 'isoform_prevalence', 'reference_protein', 'variant_protein', 'splicing_engine']]
 
 
 def process_splicing_path(new_boundaries, reference_transcript, mutated_transcript,

{geney-1.3.75.dist-info → geney-1.3.77.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.75
+Version: 1.3.77
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.75.dist-info → geney-1.3.77.dist-info}/RECORD

@@ -11,7 +11,7 @@ geney/graphic_utils.py,sha256=oMsBpB9YeEn96gGpKh4MmtagJffWZbk-xPrIwHvkFhA,11016
 geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
 geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
-geney/oncosplice.py,sha256=OptwyMhTaL5ptmdPxyuC2Iwm4feQf0n1ZjN0o9hwZ1w,32051
+geney/oncosplice.py,sha256=hADoNLoIt_f6O2lnFL0YpIOam3mOBy0BLJUNzV4npoc,32355
 geney/pangolin_utils.py,sha256=9jdBXlOcRaUdfi-UpUxHA0AkTMZkUF-Lt7HVZ1nEm3s,2973
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
@@ -25,7 +25,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
 geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4woLFSHroWIETc,4448
 geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFWDCD9cujQ_AlZO-iiOvBl82hqE,1165
 geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
-geney-1.3.75.dist-info/METADATA,sha256=RJ7URjz5xQLQy1P8fISap3pWB7qdvknUp-c2Zjgtk9I,990
-geney-1.3.75.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.75.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.75.dist-info/RECORD,,
+geney-1.3.77.dist-info/METADATA,sha256=7eMKlyiIIgYM794hncNt_lj1fyK6KzWc5zbTb8O4bw0,990
+geney-1.3.77.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.77.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.77.dist-info/RECORD,,