geney 1.3.8__py2.py3-none-any.whl → 1.3.9__py2.py3-none-any.whl

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Files changed (6) hide show
  1. geney/oncosplice.py +1 -1
  2. geney/splicing_utils.py +2 -2
  3. {geney-1.3.8.dist-info → geney-1.3.9.dist-info}/METADATA +1 -1
  4. {geney-1.3.8.dist-info → geney-1.3.9.dist-info}/RECORD +6 -6
  5. {geney-1.3.8.dist-info → geney-1.3.9.dist-info}/WHEEL +0 -0
  6. {geney-1.3.8.dist-info → geney-1.3.9.dist-info}/top_level.txt +0 -0
geney/oncosplice.py CHANGED
@@ -365,7 +365,7 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
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  report['isoform_id'] = short_hash_of_list(mutated_transcript.exons)
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  report['isoform_prevalence'] = new_boundaries['path_weight']
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  report['full_missplicing'] = missplicing.aberrant_splicing
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- report['missplicing'] = missplicing.max_delta
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+ report['missplicing'] = missplicing.max_delta()
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  report['reference_resemblance'] = reference_gene_proteins.get(mutated_transcript.protein, None)
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  results.append(report)
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geney/splicing_utils.py CHANGED
@@ -204,7 +204,7 @@ def find_transcript_splicing(transcript, engine: str = 'spliceai') -> Tuple[Dict
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  return donor_probs, acceptor_probs
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- def find_transcript_missplicing(mut_id, transcript='primary', threshold=0.5, engine='spliceai', organism='hg38'):
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+ def find_transcript_missplicing(mut_id, transcript=None, threshold=0.5, engine='spliceai', organism='hg38'):
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  gene = Gene.from_file(mut_id.split(':')[0], organism=organism)
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  reference_transcript = gene.transcript(transcript) if transcript is not None else gene.transcript()
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  variant_transcript = reference_transcript.clone()
@@ -217,7 +217,7 @@ def find_transcript_missplicing(mut_id, transcript='primary', threshold=0.5, eng
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  for mutation in mutations:
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  variant_transcript.mutate(mutation, inplace=True)
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- return find_transcript_missplicing_seqs(reference_transcript.get_context(center, 7500), variant_transcript.get_context(center, 7500), reference_transcript.donors, reference_transcript.acceptors, threshold=threshold, engine=engine)
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+ return find_transcript_missplicing_seqs(reference_transcript.pre_mrna.get_context(center, 7500), variant_transcript.pre_mrna.get_context(center, 7500), reference_transcript.donors, reference_transcript.acceptors, threshold=threshold, engine=engine)
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  # from functools import reduce
{geney-1.3.8.dist-info → geney-1.3.9.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: 1.3.8
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+ Version: 1.3.9
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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-1.3.8.dist-info → geney-1.3.9.dist-info}/RECORD RENAMED
@@ -10,12 +10,12 @@ geney/graphic_utils.py,sha256=oMsBpB9YeEn96gGpKh4MmtagJffWZbk-xPrIwHvkFhA,11016
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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=YXq-sZ_59epfi7WKP49SNjEQpd-9eViIJ06mRSqeg_M,22341
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+ geney/oncosplice.py,sha256=LOgpdsTC1JotC2qFnqNMefl0t77vvWCJ5XctZsbrLNA,22343
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  geney/pangolin_utils.py,sha256=i5j5vEMCWOTIa1mRP2377BAhlUFZjHBzTQBips4lA_4,2934
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  geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
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  geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
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  geney/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
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- geney/splicing_utils.py,sha256=s3FW4n9Bi_kkeBhrx-2cVBedyda5ddC0Oy4i3jADBj4,26365
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+ geney/splicing_utils.py,sha256=YDhYtns6pVHmOfk4Z1AC-acA1kKAqKZmJ-P2EZS946k,26378
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  geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
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  geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
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  geney/tis_utils.py,sha256=2makfGfVlDFVIbxzXE85AY9jmAjcNmxyIAxjvkRA5LY,7396
@@ -24,7 +24,7 @@ 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-1.3.8.dist-info/METADATA,sha256=bBSwVDRmEnnW12pS2BcRm6blCcUuacYCn5Yd6yBngCY,994
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- geney-1.3.8.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
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- geney-1.3.8.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.3.8.dist-info/RECORD,,
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+ geney-1.3.9.dist-info/METADATA,sha256=tkuruBdfjmOTkAz6lM3xZ_nAEXm5Vh4wpaP5FihlTvk,994
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+ geney-1.3.9.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
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+ geney-1.3.9.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.3.9.dist-info/RECORD,,
{geney-1.3.8.dist-info → geney-1.3.9.dist-info}/WHEEL RENAMED
File without changes