geney 1.3.29__py2.py3-none-any.whl → 1.3.30__py2.py3-none-any.whl

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Files changed (5) hide show
  1. geney/Gene.py +9 -0
  2. {geney-1.3.29.dist-info → geney-1.3.30.dist-info}/METADATA +1 -1
  3. {geney-1.3.29.dist-info → geney-1.3.30.dist-info}/RECORD +5 -5
  4. {geney-1.3.29.dist-info → geney-1.3.30.dist-info}/WHEEL +0 -0
  5. {geney-1.3.29.dist-info → geney-1.3.30.dist-info}/top_level.txt +0 -0
geney/Gene.py CHANGED
@@ -138,6 +138,9 @@ class Gene:
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  if tid is None:
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  tid = self.primary_transcript
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+ if tid is None:
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+ return Transcript()
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+
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  if tid not in self.transcripts:
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  raise AttributeError(f"Transcript '{tid}' not found in gene '{self.gene_name}'.")
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@@ -170,6 +173,12 @@ class Gene:
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  self._primary_transcript = protein_coding[0]
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  return self._primary_transcript
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+ # # Fallback 2: find a proitein coding transcript that is not fully defined
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+ # protein_coding = [k for k, v in self.transcripts.items() if v.get('transcript_biotype') == 'protein_coding_CDS_not_defined']
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+ # if protein_coding:
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+ # self._primary_transcript = protein_coding[0]
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+ # return self._primary_transcript
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+
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  # No primary or protein-coding transcript found
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  self._primary_transcript = None
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  return None
{geney-1.3.29.dist-info → geney-1.3.30.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: geney
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- Version: 1.3.29
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+ Version: 1.3.30
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  Summary: A Python package for gene expression modeling.
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  Home-page: https://github.com/nicolaslynn/geney
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  Author: Nicolas Lynn
{geney-1.3.29.dist-info → geney-1.3.30.dist-info}/RECORD RENAMED
@@ -1,5 +1,5 @@
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  geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
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- geney/Gene.py,sha256=JGWtfA6-d1W3I9YRASwaF8vaZ6CCuY0KEawQNdloIqY,6259
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+ geney/Gene.py,sha256=1pqKI3hGZndi7VY4j66ObhJjnz8YiNtBLGJTIHWVujA,6670
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  geney/SeqMats.py,sha256=aLpqd7RJSEU07jdPXpbtZPeb2D9BxrZuW6BTkcXpNE4,18819
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  geney/Transcript.py,sha256=eRZXVVxDVBbv0l385bnAOBFRBSzBwppXcbBq8KXkwlo,14443
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  geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
@@ -25,7 +25,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
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  geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4woLFSHroWIETc,4448
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  geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFWDCD9cujQ_AlZO-iiOvBl82hqE,1165
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  geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
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- geney-1.3.29.dist-info/METADATA,sha256=Chxu6iycgZPwhUI1X7-VrCdFoZC3TQqF3MMnX6SS9Ps,990
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- geney-1.3.29.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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- geney-1.3.29.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.3.29.dist-info/RECORD,,
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+ geney-1.3.30.dist-info/METADATA,sha256=ZS6Ft5TJYV5WFTOM47ny7m7eSA76C2EmCEMD2yuBhcQ,990
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+ geney-1.3.30.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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+ geney-1.3.30.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.3.30.dist-info/RECORD,,
{geney-1.3.29.dist-info → geney-1.3.30.dist-info}/WHEEL RENAMED
File without changes