geney 1.4.41__py3-none-any.whl → 1.4.42__py3-none-any.whl

geney/__init__.py

@@ -15,6 +15,7 @@ from .pipelines import (
     max_splicing_delta,
     oncosplice_pipeline_single_transcript,  # backwards compat
 )
+# from .samples import *
 
 __all__ = [
     "Mutation",
@@ -35,4 +36,5 @@ __all__ = [
 
 
 mut_id = 'KRAS:12:25227343:G:T'
-epistasis_id = 'KRAS:12:25227343:G:T|KRAS:12:25227344:A:T'
+epistasis_id = 'KRAS:12:25227343:G:T|KRAS:12:25227344:A:T'
+

geney/oncosplice.py

@@ -388,9 +388,10 @@ class Oncosplice:
         analysis_dict = {
             'reference_protein': self.reference_protein,
             'variant_protein': self.variant_protein,
+            'aligned_reference_protein': self.alignment.seqA,
+            'aligned_variant_protein': self.alignment.seqB,
             'reference_length': len(self.reference_protein),
             'variant_length': len(self.variant_protein),
-            # 'alignment_length': len(self.alignment.seqA),
             'oncosplice_score': self.score,
             'percentile': self.percentile,
             'number_of_deletions': len(self.deletions),

geney/pipelines.py

@@ -34,6 +34,10 @@ def oncosplice_pipeline(
         .generate_protein()
     )
 
+    # Truncate protein at first stop codon
+    if '*' in reference_transcript.protein:
+        reference_transcript.protein = reference_transcript.protein[:reference_transcript.protein.index('*') + 1]
+
     tl = TranscriptLibrary(reference_transcript, m)
     central_pos = m.central_position
 
@@ -71,6 +75,7 @@ def oncosplice_pipeline(
                 pd.Series({
                     "reference_mrna": reference_transcript.mature_mrna.seq,
                     "variant_mrna": variant_transcript.mature_mrna.seq,
+                    "conservation_vector": onco.conservation_vector,
                 }),
                 onco.get_analysis_series(),
             ])
@@ -123,6 +128,10 @@ def max_splicing_delta(
         .generate_protein()
     )
 
+    # Truncate protein at first stop codon
+    if '*' in reference_transcript.protein:
+        reference_transcript.protein = reference_transcript.protein[:reference_transcript.protein.index('*') + 1]
+
     tl = TranscriptLibrary(reference_transcript, m)
     splicing_results = tl.predict_splicing(
         m.central_position, engine=splicing_engine, inplace=True

geney/splice_graph.py

@@ -422,6 +422,10 @@ class SpliceSimulator:
             t.path_hash = _short_hash(tuple(donors + acceptors))
             t.generate_mature_mrna().generate_protein()
 
+            # Truncate protein at first stop codon
+            if '*' in t.protein:
+                t.protein = t.protein[:t.protein.index('*') + 1]
+
             # Filter out implausible IR paths (where cryptic sites compensate)
             if self._is_implausible_ir_path(t):
                 continue

{geney-1.4.41.dist-info → geney-1.4.42.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: geney
-Version: 1.4.41
+Version: 1.4.42
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

geney-1.4.42.dist-info/RECORD

@@ -0,0 +1,11 @@
+geney/__init__.py,sha256=AIKhk1FPsnObK-GrBXU1T780KX0i1K-q34r4zh3ojok,993
+geney/engines.py,sha256=9_oNsoluJsjdLC3cyWttjHF3cuQoy65FWgS4r7ehzek,14296
+geney/oncosplice.py,sha256=rEVNhHugtzOvwicdjzRqbcyWG-KM0JIgvQa9Mpo23p4,18076
+geney/pipelines.py,sha256=ply3zS5zgA-4I-vCRF0_bJmZ4CtIrzSSpUQOsh3AZmo,4469
+geney/splice_graph.py,sha256=BnJDSOq3mePC0I0cFyfXyUyePANwhrk3LlBPoV1vzSs,24081
+geney/transcripts.py,sha256=BBgyeqF4jeIiHaD_bXxgOTXz19kdUgjcPVo4ClpcSUg,2594
+geney/variants.py,sha256=vjbiBH-duZ4TJZyXwXbQ_VmJxCFafjeDwLNTZg3ubSc,11832
+geney-1.4.42.dist-info/METADATA,sha256=ZTuy2ydDiv2Pndu1R1TADe_3kA1FN7xbI51NdiZmQgs,972
+geney-1.4.42.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+geney-1.4.42.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.4.42.dist-info/RECORD,,

{geney-1.4.41.dist-info → geney-1.4.42.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

geney-1.4.41.dist-info/RECORD

@@ -1,11 +0,0 @@
-geney/__init__.py,sha256=nkhniqCNWJzrb7xHgTDFEXSvRVdggb9ZCJ7ih7HEYq8,966
-geney/engines.py,sha256=9_oNsoluJsjdLC3cyWttjHF3cuQoy65FWgS4r7ehzek,14296
-geney/oncosplice.py,sha256=eGQQl9ftmoFENMYBWoJtenKWmzyxR9N1of5cZst_bHQ,18014
-geney/pipelines.py,sha256=gsy-gmHIi260SC5MKQ9IBSE0wko8Tvd7IC3wj083mPQ,3996
-geney/splice_graph.py,sha256=PANtLUAQiz578NZwxVlTSgboetnToHnQSkYpT0zbi_w,23931
-geney/transcripts.py,sha256=BBgyeqF4jeIiHaD_bXxgOTXz19kdUgjcPVo4ClpcSUg,2594
-geney/variants.py,sha256=vjbiBH-duZ4TJZyXwXbQ_VmJxCFafjeDwLNTZg3ubSc,11832
-geney-1.4.41.dist-info/METADATA,sha256=zuzWKIEeHSaFr08eRUjq3ZSiloOepcCD_QRG5ifS8j0,972
-geney-1.4.41.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-geney-1.4.41.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.4.41.dist-info/RECORD,,