geney 1.2.36__py2.py3-none-any.whl → 1.2.38__py2.py3-none-any.whl

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Files changed (6) hide show
  1. geney/oncosplice.py +2 -2
  2. geney/tis_utils.py +1 -1
  3. {geney-1.2.36.dist-info → geney-1.2.38.dist-info}/METADATA +1 -1
  4. {geney-1.2.36.dist-info → geney-1.2.38.dist-info}/RECORD +6 -6
  5. {geney-1.2.36.dist-info → geney-1.2.38.dist-info}/WHEEL +0 -0
  6. {geney-1.2.36.dist-info → geney-1.2.38.dist-info}/top_level.txt +0 -0
geney/oncosplice.py CHANGED
@@ -400,7 +400,7 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, primary_tran
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  sorted(cons_vector).index(next(x for x in sorted(cons_vector) if x >= affected_cons_scores)) / len(
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  cons_vector))
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- report = OncospliceAnnotator(reference_transcript, transcript, mutation)
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+ report = {} #OncospliceAnnotator(reference_transcript, transcript, mutation)
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  report['mut_id'] = mut_id
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  report['oncosplice_score'] = affected_cons_scores
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  report['percentile'] = percentile
@@ -489,7 +489,7 @@ async def oncosplice_prototype(mut_id, splicing_threshold=0.5, protein_coding=Tr
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  sorted(cons_vector).index(next(x for x in sorted(cons_vector) if x >= affected_cons_scores)) / len(
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  cons_vector))
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- out = domains_df.apply(lambda row: inspect_domain(row, va, vb), axis=1)
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+ out = domains_df.apply(lambda row: inspect_domain(row, modified_positions, cons_vector), axis=1)
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  domains_affected = '+'.join([f'{a}:{b}' for a, b in list(zip(out.domain_identifier, out.score))])
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  report = OncospliceAnnotator(reference_transcript, transcript, mutation)
geney/tis_utils.py CHANGED
@@ -97,7 +97,7 @@ def seq_matrix(seq_list):
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  return tensor
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- def build_titer_model(TITER_path=config['titer_path']):
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+ def build_titer_model(TITER_path=config['hg38']['titer_path']):
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  print('Building TITER model...')
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  from tensorflow.keras.constraints import MaxNorm
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  from tensorflow.keras.layers import Conv1D, MaxPool1D, LSTM, Dropout, Flatten, Dense, Activation
{geney-1.2.36.dist-info → geney-1.2.38.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: 1.2.36
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+ Version: 1.2.38
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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-1.2.36.dist-info → geney-1.2.38.dist-info}/RECORD RENAMED
@@ -6,7 +6,7 @@ geney/graphic_utils.py,sha256=tjm6IDQ1BdfSeuPYzjlqAUHFQoDYH9jXTzJjKFS4Hh4,11078
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  geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
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  geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
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  geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
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- geney/oncosplice.py,sha256=QETLNIzc3T1CYausLD3W_jCSJveDkg2F6WnIMagVLT0,22536
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+ geney/oncosplice.py,sha256=Ph8AMR2L9wjh3Gl3X58Dd8F1ea4on9jXIxg7EO0zVEU,22565
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  geney/pangolin_utils.py,sha256=ETTGpuaQgdZ1v8H0NP8sbTEfGWu0VXUFUS7wsURsTc4,2991
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  geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
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  geney/seqmat_utils.py,sha256=YV5DFLbfjXLIswPGvqK1-eEfwn9TUby0b2kewdGAKws,18372
@@ -14,13 +14,13 @@ geney/spliceai_utils.py,sha256=gIGPC8u3J15A7EQrk2Elho5PbF9MmUUNopGGH-eEV8s,1873
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  geney/splicing_utils.py,sha256=q47EdcsHrp4aLIPVWvkGBJSzS3l3DKiD9DNDsPpZdHk,16075
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  geney/survival_utils.py,sha256=2CAkC2LsspicHIdrqsiPnjgvpr5KHDUfLFFqnRbPJqs,5762
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  geney/tcga_utils.py,sha256=vXSMf1OxoF_AdE_rMguy_BoYaart_E1t4FFMx2DS1Ak,15585
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- geney/tis_utils.py,sha256=e66NzWbyBKVk0TvMJqdFzKJ5TGNLMMNTkWd1t97gZpw,8039
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+ geney/tis_utils.py,sha256=Oz54dgAjc1PEikp4Snh6qlpT-8eVJDWhM_k0aJAQvFM,8047
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  geney/utils.py,sha256=EsKvBM-Nz2a3_4ZAhF4Dxd4PwT7_6YYKpxEN4LLgg10,2174
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  geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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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-1.2.36.dist-info/METADATA,sha256=dNrCldyLp6EKEXolQ00IunL-Q-s5idxQLNHYFaLmVVs,948
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- geney-1.2.36.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
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- geney-1.2.36.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.2.36.dist-info/RECORD,,
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+ geney-1.2.38.dist-info/METADATA,sha256=a5g8X4PPpand3B4nvkbemKP4Sj066AVa7AqIjLBEGSU,948
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+ geney-1.2.38.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
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+ geney-1.2.38.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.2.38.dist-info/RECORD,,
{geney-1.2.36.dist-info → geney-1.2.38.dist-info}/WHEEL RENAMED
File without changes