geney 1.2.7__py2.py3-none-any.whl → 1.2.8__py2.py3-none-any.whl

geney/oncosplice.py

@@ -1033,7 +1033,7 @@ class PredictSpliceAI:
             # elif isinstance(gene_data, Transcript):
 
             # self.missplicing = run_spliceai_transcript(self.modification, transcript_data=gene_data, sai_mrg_context=sai_mrg_context, min_coverage=min_coverage, sai_threshold=0.1)
-            ref_transcript, var_transcript = Gene(gene_data.gene, organism='mm39'), Gene(gene_data.gene, variation=mutation, organism='mm39')
+            ref_transcript, var_transcript = Gene(mutation.split(':')[0], organism='mm39'), Gene(mutation.split(':')[0], variation=mutation, organism='mm39')
             self.missplicing = find_transcript_missplicing(self.modification, ref_transcript, var_transcript, context=sai_mrg_context+min_coverage, threshold=threshold,
                                 engine=engine)
             if save_results:
@@ -1503,7 +1503,7 @@ def moving_average_conv(vector, window_size, factor=1):
 
     return np.convolve(vector, np.ones(window_size), mode='same') / window_size
 
-def oncosplice(mut_id, sai_threshold=0.5, protein_coding=True, primary_transcript=False, window_length=13, save_spliceai_results=False, force_spliceai=False, organism='hg38'):
+def oncosplice(mut_id, sai_threshold=0.5, protein_coding=True, primary_transcript=False, window_length=13, save_spliceai_results=False, force_spliceai=False, organism='hg38', engine='spliceai'):
     mutation = Variations(mut_id)
     # try:
     reference_gene = Gene(mutation.gene, organism=organism)
@@ -1520,7 +1520,7 @@ def oncosplice(mut_id, sai_threshold=0.5, protein_coding=True, primary_transcrip
             continue
 
         cons_vector = transform_conservation_vector(reference.cons_vector, window=window_length)
-        missplicing_obj = PredictSpliceAI(mutation, reference, threshold=sai_threshold, force=force_spliceai, save_results=save_spliceai_results)
+        missplicing_obj = PredictSpliceAI(mutation, reference, threshold=sai_threshold, force=force_spliceai, save_results=save_spliceai_results, engine=engine)
         missplicing = missplicing_obj.apply_sai_threshold_primary(threshold=sai_threshold)
 
         for i, new_boundaries in enumerate(develop_aberrant_splicing(variant, missplicing)):

{geney-1.2.7.dist-info → geney-1.2.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.7
+Version: 1.2.8
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.7.dist-info → geney-1.2.8.dist-info}/RECORD

@@ -9,7 +9,7 @@ geney/gtex.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
 geney/netchop.py,sha256=AMiy9YsdTmX4B3k3Y5Yh7EmoGAojM1O3AzhPKOiB--g,3050
-geney/oncosplice.py,sha256=8tV8Wzz_I3CNGgeNNqhJvDOb1A3slzsyk9mnRQXuC-c,77329
+geney/oncosplice.py,sha256=NhC164g0hzuV-hxMwlVtpXFxp067Mq_fnQUhn6vKK5A,77379
 geney/oncosplice_mouse.py,sha256=LYLOukI9qI1IBkyl1qVRFR5d1NAw7Orlj8Zth-4xCW8,12962
 geney/oncosplice_pipeline.py,sha256=hpGqFHOdn8i8tvvs1-t3-G9Ko18zInwoDXBJbbrfbC4,68036
 geney/performance_utils.py,sha256=FQt7rA4r-Wuq3kceCxsSuMfj3wU1tMG8QnbL59aBohs,4700
@@ -45,7 +45,7 @@ geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFW
 geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
 geney/translation_termination/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 geney/translation_termination/tts_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-geney-1.2.7.dist-info/METADATA,sha256=cCD7LSrUBVp3Hr7HtUFTEFuKFAeD1Yq3Zoyh31CZTfk,1198
-geney-1.2.7.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-geney-1.2.7.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.7.dist-info/RECORD,,
+geney-1.2.8.dist-info/METADATA,sha256=2Eu8FxQqLudUMoNG0rt-l2OwT8cikYNb1S407dsYG7E,1198
+geney-1.2.8.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+geney-1.2.8.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.8.dist-info/RECORD,,