geney 1.3.49__py2.py3-none-any.whl → 1.3.51__py2.py3-none-any.whl

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Files changed (5) hide show
  1. geney/SeqMats.py +6 -4
  2. {geney-1.3.49.dist-info → geney-1.3.51.dist-info}/METADATA +1 -1
  3. {geney-1.3.49.dist-info → geney-1.3.51.dist-info}/RECORD +5 -5
  4. {geney-1.3.49.dist-info → geney-1.3.51.dist-info}/WHEEL +0 -0
  5. {geney-1.3.49.dist-info → geney-1.3.51.dist-info}/top_level.txt +0 -0
geney/SeqMats.py CHANGED
@@ -362,13 +362,15 @@ class SeqMat:
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  temp = SeqMat(temp) # .drop_indices()
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  raw_seq = temp.seq # Extract the raw sequence
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  pattern = re.compile(r"(?:[NACGT]{3})*?(TAA|TAG|TGA)")
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- match = pattern.match(raw_seq)
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- if match:
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- stop_index = match.end()
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+ # match = pattern.match(raw_seq)
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+ match = [(m.group(), m.start()) for m in re.finditer(r"(?:[NACGT]{3})*?(TAA|TAG|TGA)", raw_seq) if
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+ m.start() % 3 == 0]
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+ if len(match) > 0:
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+ stop_index = match[0][-1] #.end()
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  else:
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  stop_index = len(raw_seq)
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  end_index = stop_index
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- assert end_index % 3 == 0, f"{end_index} is not a multiple of 3"
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+ assert (end_index+1) % 3 == 0, f"{end_index} is not a multiple of 3"
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  return SeqMat(temp.seqmat[:, :end_index])
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  def translate(self, tis_index):
{geney-1.3.49.dist-info → geney-1.3.51.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: 1.3.49
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+ Version: 1.3.51
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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-1.3.49.dist-info → geney-1.3.51.dist-info}/RECORD RENAMED
@@ -1,6 +1,6 @@
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  geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
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  geney/Gene.py,sha256=nMWJjoQaiVFm2iRjoiq7ghZqnXtW0tJDcq2S0AyOIvY,6883
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- geney/SeqMats.py,sha256=pdnwg-RDxeZ4U7DCjZ41REll-HISVf_unXNsfbKVq9w,19039
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+ geney/SeqMats.py,sha256=PMSnGquc36vTxSbyn3DdQ11-wrZeu2asUo--gfYBJLc,19209
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  geney/Transcript.py,sha256=CpfxYkuCwFILozrtLuiWnlr1mRnMKn4o84HVJislgYs,14499
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  geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
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  geney/_mutation_utils.py,sha256=dHssUsnii_mf-wuRoMmF13UlD7k3ml_VwQMItTYnXpU,1132
@@ -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-1.3.49.dist-info/METADATA,sha256=1tglGOcOnNBzE0M3lN2mo_J26uWPPNYFN_pNHVHHQiA,990
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- geney-1.3.49.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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- geney-1.3.49.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.3.49.dist-info/RECORD,,
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+ geney-1.3.51.dist-info/METADATA,sha256=E0XM_zYhp9lObUL9fUG3F0XzualauK-DIeAPcVTC5ko,990
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+ geney-1.3.51.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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+ geney-1.3.51.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.3.51.dist-info/RECORD,,
{geney-1.3.49.dist-info → geney-1.3.51.dist-info}/WHEEL RENAMED
File without changes