geney 1.3.57__py2.py3-none-any.whl → 1.3.59__py2.py3-none-any.whl

geney/SeqMats.py

@@ -300,6 +300,10 @@ class SeqMat:
     def raw_indices(self):
         return self.seqmat[self.ROW_INDS, :] + (self.seqmat[self.ROW_SUPERINDS, :] / 10)
 
+    @property
+    def filter(self):
+        return self.seqmat[:, self.seqmat[self.ROW_SEQ, :] != 5]
+
 
     def mutate(self, mut, inplace=False):
         """
@@ -357,15 +361,19 @@ class SeqMat:
         if tis_index not in self.indices:
             return SeqMat.from_seq({'seq': ''})
 
-        temp = self.seqmat[:, self._rel_index(tis_index):]
-        temp = temp[:, temp[0, :] != 5]
-        temp = SeqMat(temp)  # .drop_indices()
-        raw_seq = temp.seq  # Extract the raw sequence
-        pattern = re.compile(r"(?:[NACGT]{3})*?(TAA|TAG|TGA)")
+        raw_seq = SeqMat(self.seqmat[:, self._rel_index(tis_index):])
+        raw_seq = SeqMat(raw_seq.filter)
+
+        # temp = temp[:, temp[0, :] != 5]
+        # temp = SeqMat(temp)  # .drop_indices()
+        # 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()+1) for m in re.finditer(r"(?:[NACGT]{3})*?(TAA|TAG|TGA)", raw_seq) if
-                 (m.start()+1) % 3 == 0]
+        print(raw_seq.rawseq)
+        match = [(m.group(), m.start()+1) for m in re.finditer(r"(?:[NACGT]{3})*?(TAA|TAG|TGA)", raw_seq.seq)]# if
+                 # (m.start()+1) % 3 == 0]
 
+        print(match)
         if len(match) > 0:
             stop_index = match[0][-1] #.end()
         else:
@@ -373,7 +381,7 @@ class SeqMat:
 
         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])
+        return SeqMat(raw_seq.seqmat[:, :end_index])
 
     def translate(self, tis_index):
         """

geney/oncosplice.py

@@ -338,9 +338,9 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
             mutated_transcript.mutate(mutation, inplace=True)
 
         reference_transcript.generate_mature_mrna().generate_protein()
-        if ('*' in reference_transcript.protein[:-1]):
-            print(f"> Errors in reference transcript {reference_transcript.transcript_id}")
-            continue
+        # if ('*' in reference_transcript.protein[:-1]):
+        #     print(f"> Errors in reference transcript {reference_transcript.transcript_id}")
+        #     continue
 
         if len(reference_transcript.protein) < window_length:
             print(f"> Window length issue {reference_transcript.transcript_id}")

{geney-1.3.57.dist-info → geney-1.3.59.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.57
+Version: 1.3.59
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.57.dist-info → geney-1.3.59.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=AKR1EhyDhOaEhavrkXSrVjYsohB6Qvsq11Udy7SGwvs,19238
+geney/SeqMats.py,sha256=xiX6c4o0Imb00dzTmSgX4spvn7m0lB6IBMr0Sn2WUHE,19463
 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=G9OB6OPy6HV9RRBUUWnJqOLLsREpHCLOoNDn6m6ay0M,24698
+geney/oncosplice.py,sha256=9_Eo5fL68CosTj6yTfh3UjCXHprhzqHFRL21WRicMRs,24704
 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-1.3.57.dist-info/METADATA,sha256=oZcH7DyAdYHd-U5r06RTp7jPnUDdFH-G3-3CCJtUNOg,990
-geney-1.3.57.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.57.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.57.dist-info/RECORD,,
+geney-1.3.59.dist-info/METADATA,sha256=h5ITzoYHQSPAse3aAS7Xpx97O0aEkQVCZoB-iE_NXIY,990
+geney-1.3.59.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.59.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.59.dist-info/RECORD,,