geney 1.3.53__py2.py3-none-any.whl → 1.3.55__py2.py3-none-any.whl

geney/SeqMats.py

@@ -363,13 +363,14 @@ class SeqMat:
         raw_seq = temp.seq  # Extract the raw sequence
         pattern = re.compile(r"(?:[NACGT]{3})*?(TAA|TAG|TGA)")
         # match = pattern.match(raw_seq)
-        match = [(m.group(), m.start()) for m in re.finditer(r"(?:[NACGT]{3})*?(TAA|TAG|TGA)", raw_seq) if
-                 (m.start() + 1) % 3 == 0]
+        match = [(m.group(), m.start()+1) for m in re.finditer(r"(?:[NACGT]{3})*?(TAA|TAG|TGA)", raw_seq) if
+                 (m.start()+1) % 3 == 0]
 
         if len(match) > 0:
             stop_index = match[0][-1] #.end()
         else:
-            stop_index = len(raw_seq)
+            stop_index = len(raw_seq) - (len(raw_seq) % 3)
+
         end_index = stop_index
         # assert (end_index+1) % 3 == 0, f"{end_index} is not a multiple of 3"
         return SeqMat(temp.seqmat[:, :end_index])

geney/oncosplice.py

@@ -319,14 +319,15 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
 
     results = []
     for reference_transcript in tqdm(gene, desc=f'Processing {mut_id}...'):
-        if (cons_required and not reference_transcript.cons_available) or (
-                protein_coding and not reference_transcript.transcript_biotype == 'protein_coding'):
-            print("Missing either protein coding or conservation...")
+        # if (cons_required and not reference_transcript.cons_available) or (
+        #         protein_coding and not reference_transcript.transcript_biotype == 'protein_coding'):
+        if protein_coding and not reference_transcript.transcript_biotype == 'protein_coding':
+            print("Not protein coding...")
             continue
 
         current_mutations = [m for m in mutations if m in reference_transcript]
         if len(current_mutations) == 0:
-            print("No mutations within transcript...")
+            print(f"No mutations within transcript ({reference_transcript.transcript_start} > {reference_transcript.transcript_end})...")
             continue
 
         center = np.mean([m.indices[0] for m in current_mutations]) // 1

{geney-1.3.53.dist-info → geney-1.3.55.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.53
+Version: 1.3.55
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.53.dist-info → geney-1.3.55.dist-info}/RECORD

@@ -1,6 +1,6 @@
 geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
 geney/Gene.py,sha256=nMWJjoQaiVFm2iRjoiq7ghZqnXtW0tJDcq2S0AyOIvY,6883
-geney/SeqMats.py,sha256=XWVs1Mv4Y8Kblm2cFPPflPyWQOde433RoS6odNEcHJM,19216
+geney/SeqMats.py,sha256=AKR1EhyDhOaEhavrkXSrVjYsohB6Qvsq11Udy7SGwvs,19238
 geney/Transcript.py,sha256=CpfxYkuCwFILozrtLuiWnlr1mRnMKn4o84HVJislgYs,14499
 geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
 geney/_mutation_utils.py,sha256=dHssUsnii_mf-wuRoMmF13UlD7k3ml_VwQMItTYnXpU,1132
@@ -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=ghEY6HEJKpQrJYT26sVbXpTuqMrR4YmMV7JuAL4a8jQ,24424
+geney/oncosplice.py,sha256=-WlZRRkrZGF9hNT9CEJJUBxeeR0lKy2Yo9kzjPYC8Ok,24579
 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-1.3.53.dist-info/METADATA,sha256=Lmc1Mb5jyLN9bJ3iivUTCyb2YWSpyXAMCXfITMSPVtY,990
-geney-1.3.53.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.53.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.53.dist-info/RECORD,,
+geney-1.3.55.dist-info/METADATA,sha256=kLdJrug4ERJSEvhw28dSYyHv7Ax4PYtWtcRfvlFVpsY,990
+geney-1.3.55.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.55.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.55.dist-info/RECORD,,