geney 1.4.25__py2.py3-none-any.whl → 1.4.27__py2.py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (7) hide show
  1. geney/pipelines.py +3 -1
  2. geney/utils/SeqMats.py +1 -1
  3. geney/utils/TranscriptLibrary.py +2 -2
  4. {geney-1.4.25.dist-info → geney-1.4.27.dist-info}/METADATA +1 -1
  5. {geney-1.4.25.dist-info → geney-1.4.27.dist-info}/RECORD +7 -7
  6. {geney-1.4.25.dist-info → geney-1.4.27.dist-info}/WHEEL +0 -0
  7. {geney-1.4.25.dist-info → geney-1.4.27.dist-info}/top_level.txt +0 -0
geney/pipelines.py CHANGED
@@ -40,7 +40,9 @@ def oncosplice_pipeline_single_transcript(mut_id, transcript_id=None, splicing_e
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  report = []
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  for variant_transcript, isoform_metadata in ss.get_viable_transcripts(metadata=True):
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  onco = Oncosplice(reference_transcript.protein, variant_transcript.protein, reference_transcript.cons_vector)
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- report.append(pd.concat([base_report, ss_metadata, isoform_metadata, onco.get_analysis_series()]))
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+ report.append(pd.concat([base_report, ss_metadata, isoform_metadata,
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+ pd.Series({'reference_mrna': reference_transcript.mature_mrna.seq, 'variant_mrna': variant_transcript.mature_mrna.seq}),
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+ onco.get_analysis_series()]))
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  return pd.DataFrame(report)
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geney/utils/SeqMats.py CHANGED
@@ -165,7 +165,7 @@ class SeqMat:
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  # only_snps: bool = False
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  # ) -> SeqMat:
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- def apply_mutation(
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+ def apply_mutations(
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  self,
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  mutations: Union[Tuple[float, str, str], List[Tuple[float, str, str]]] = None,
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  *,
geney/utils/TranscriptLibrary.py CHANGED
@@ -11,10 +11,10 @@ class TranscriptLibrary:
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  # Apply all mutations to 'event'
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  for i, (pos, ref, alt) in enumerate(mutations):
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- self.event.pre_mrna.apply_mutation(pos, ref, alt)
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+ self.event.pre_mrna.apply_mutations((pos, ref, alt))
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  if len(mutations) > 1:
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  t = reference_transcript.clone()
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- t.pre_mrna.apply_mutation(pos, ref, alt)
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+ t.pre_mrna.apply_mutations((pos, ref, alt))
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  self._transcripts[f'mut{i+1}'] = t
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  setattr(self, f'mut{i+1}', t)
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{geney-1.4.25.dist-info → geney-1.4.27.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: 1.4.25
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+ Version: 1.4.27
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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-1.4.25.dist-info → geney-1.4.27.dist-info}/RECORD RENAMED
@@ -23,7 +23,7 @@ geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
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  geney/immune_utils.py,sha256=b-8dRcCti7xsU7RG3op18lkSnAD8dp_BymGaR-hbNcI,5272
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  geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
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  geney/pangolin_utils.py,sha256=9jdBXlOcRaUdfi-UpUxHA0AkTMZkUF-Lt7HVZ1nEm3s,2973
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- geney/pipelines.py,sha256=XeC4NTqxzHzrGX6HIBXe8pe4pELpjYLgTmcOt7ESN0g,2916
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+ geney/pipelines.py,sha256=p_zZjQRkcQ_MwOZWv247QVG5iNSrrV4g8BT3vJNwpZM,3103
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  geney/power_utils.py,sha256=orOhsr9vkQ-Y4nD1zHj_MmR2J3uYiUsiklqVy-5T-2M,7331
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  geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
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  geney/spliceai_utils.py,sha256=nyBnLdYs1rB-duA9lfJYM9Q2xNlvZA3I_sCJ1z5WjFw,3294
@@ -37,16 +37,16 @@ geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4w
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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/utils/Fasta_segment.py,sha256=weB5NJ65P0XiyAJCiCHx4T9sHC1pWLpuQeOy0B85gyg,11364
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- geney/utils/SeqMats.py,sha256=zymeGYvpuJOBlEBx6vrbh9b6y9t4egCmKnerrxxKU8s,17615
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+ geney/utils/SeqMats.py,sha256=PaUp6PMKYDYZ8RTodmKAmCa9ywHnkqSEqTjPoATr82k,17616
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  geney/utils/SeqMatsOld.py,sha256=syRU5DAuTh3xUfGW_qP9wlcBO5pHsG_y5PlrfXTIxUY,18502
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- geney/utils/TranscriptLibrary.py,sha256=ma_ZVPgglxXDDneEvdqxxeqxG8eSFL-zgLUXyC6BqY8,2070
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+ geney/utils/TranscriptLibrary.py,sha256=W1hv4Y8wRlmwTs3iFdn4_IqS-2suVDzZe4fwti2KbR4,2076
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  geney/utils/__init__.py,sha256=-nJ-DMx1JzP-ZCe_QuQCeM0ZYIT_16jxoXDhUaO_4Oc,714
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  geney/utils/mutation_utils.py,sha256=r-pHr56gEa5kh_DPX8MjFY3ZfYaOtyo4CUfJ5ZHlXPw,3243
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  geney/utils/pangolin_utils.py,sha256=JQSPbWxdzqGFYfWQktkfLMaMSGR28eGQhNzO7MLMe5M,6162
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  geney/utils/spliceai_utils.py,sha256=VtrIbjyQxk_3lw86eWjftRYyal9OzxArJ0GV5u_ymTg,2721
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  geney/utils/splicing_utils.py,sha256=vPCGnCPR1ooEZEHR79yFHLmRQXEJHXEQjjxpBR-YWOs,20635
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  geney/utils/utils.py,sha256=m51Vd0cEbrcIHo6_8BAuI9YSPcKRs22e5LfVd2Qj6Is,2181
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- geney-1.4.25.dist-info/METADATA,sha256=iZ5UDkA4ibY03jtqec5n4grbfchBJxsf2Qpnw7KZW5c,990
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- geney-1.4.25.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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- geney-1.4.25.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.4.25.dist-info/RECORD,,
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+ geney-1.4.27.dist-info/METADATA,sha256=m4-HDmqjW43J6QhNdel4Luy18FvL4FXAHw-zE1hPDcQ,990
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+ geney-1.4.27.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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+ geney-1.4.27.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.4.27.dist-info/RECORD,,
{geney-1.4.25.dist-info → geney-1.4.27.dist-info}/WHEEL RENAMED
File without changes