geney 1.1.6__py2.py3-none-any.whl → 1.1.7__py2.py3-none-any.whl

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Files changed (5) hide show
  1. geney/netchop.py +2 -5
  2. {geney-1.1.6.dist-info → geney-1.1.7.dist-info}/METADATA +1 -1
  3. {geney-1.1.6.dist-info → geney-1.1.7.dist-info}/RECORD +5 -5
  4. {geney-1.1.6.dist-info → geney-1.1.7.dist-info}/WHEEL +0 -0
  5. {geney-1.1.6.dist-info → geney-1.1.7.dist-info}/top_level.txt +0 -0
geney/netchop.py CHANGED
@@ -26,24 +26,21 @@ class NetChop(object):
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  the cleavage probability for each position in the sequence.
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  """
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  with tempfile.NamedTemporaryFile(dir=config_setup['NETCHOP'], suffix=".fsa", mode="w") as input_fd:
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+ print(f"Writing to {input_fd.name}...")
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  for (i, sequence) in enumerate(sequences):
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+ print(f"\tseq{i}: {sequence}")
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  input_fd.write("> %d\n" % i)
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  input_fd.write(sequence)
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  input_fd.write("\n")
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  input_fd.flush()
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- print(input_fd.__dict__)
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- print(input_fd.name)
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-
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  try:
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  output = subprocess.check_output(["netChop", input_fd.name])
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  except subprocess.CalledProcessError as e:
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  logging.error("Error calling netChop: %s:\n%s" % (e, e.output))
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  raise
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- print("here")
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  parsed = self.parse_netchop(output)
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- print("here2")
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  assert len(parsed) == len(sequences), \
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  "Expected %d results but got %d" % (
{geney-1.1.6.dist-info → geney-1.1.7.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: 1.1.6
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+ Version: 1.1.7
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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-1.1.6.dist-info → geney-1.1.7.dist-info}/RECORD RENAMED
@@ -7,7 +7,7 @@ geney/config_setup.py,sha256=SePeooA4RWAtR_KAT1-W1hkD3MT5tH6YMyp80t_RNPQ,385
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  geney/data_setup.py,sha256=DZeksRPr2ZT7bszMo33W0r3OwmqHokVXtZ4gx5Lu_Mo,10725
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  geney/gtex.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
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  geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
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- geney/netchop.py,sha256=Hy9vhcjda9JjrlMqEfQfN4UpX9Yb7nTw0fIGextK278,2998
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+ geney/netchop.py,sha256=h6hRkfYvmkU-ZI9Zeg5mW1fGUN4e97-Ar4r7aSGx7UE,2981
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  geney/oncosplice.py,sha256=Fyc_UtAhV3Pv0vk8V55rO_jnb2Dwj5sW98KVwP3PHwU,68964
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  geney/oncosplice_pipeline.py,sha256=hpGqFHOdn8i8tvvs1-t3-G9Ko18zInwoDXBJbbrfbC4,68036
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  geney/performance_utils.py,sha256=FQt7rA4r-Wuq3kceCxsSuMfj3wU1tMG8QnbL59aBohs,4700
@@ -43,7 +43,7 @@ geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFW
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  geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
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  geney/translation_termination/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  geney/translation_termination/tts_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- geney-1.1.6.dist-info/METADATA,sha256=F4-FCWvnpkBtBvtLuVBUmvTPMk06G7BhDIRs61_0naA,1130
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- geney-1.1.6.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
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- geney-1.1.6.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.1.6.dist-info/RECORD,,
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+ geney-1.1.7.dist-info/METADATA,sha256=-arp47Qb2ah8D5x0TTBDaeUNu3kFwhmzwwBdiz5J0L8,1130
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+ geney-1.1.7.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
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+ geney-1.1.7.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.1.7.dist-info/RECORD,,
{geney-1.1.6.dist-info → geney-1.1.7.dist-info}/WHEEL RENAMED
File without changes