geney 1.2.15__py2.py3-none-any.whl → 1.2.17__py2.py3-none-any.whl

geney/oncosplice.py

@@ -219,6 +219,7 @@ class Gene:
         self.gene_end = 0
         self.transcripts = {}
         self.load_from_file(find_files_by_gene_name(gene_name, organism=organism))
+        # print(f"In Gene: {variation}")
         self.variations = variation
         self.primary_tid = None
         self.organism = organism
@@ -271,7 +272,7 @@ class Gene:
 
         if tid not in self.transcripts:
             raise AttributeError(f"Transcript '{tid}' not found in gene '{self.gene_name}'.")
-        return Transcript(self.transcripts[tid], organism=self.organism)
+        return Transcript(self.transcripts[tid], organism=self.organism, variations=self.variations)
 
     def run_transcripts(self, primary_transcript=False, protein_coding=False):
         for tid, annotations in self.transcripts.items():
@@ -306,7 +307,7 @@ class Transcript:
         self.cons_vector = ''
         self.variations = None
         self.organism = organism
-        print(f"Variations: {variations}")
+        # print(f"Variations: {variations}")
         if variations:
             self.variations = Variations(variations)
 
@@ -520,7 +521,7 @@ class Transcript:
         seq, indices = self.pull_pre_mrna_pos()
         if self.variations:
             for mutation in self.variations.variants:
-                print(f"Implementing {mutation}")
+                # print(f"Implementing {mutation}")
                 seq, indices = generate_mut_variant(seq, indices, mut=mutation)
         return seq, indices
 
@@ -793,7 +794,7 @@ def find_transcript_missplicing(mutations, ref_transcript, var_transcript, conte
     start_pad, end_pad = max(0, context - (center_index - start_cutoff)), max(0, context - (end_cutoff - center_index))
     mut_seq = 'N' * start_pad + mut_seq[start_cutoff:end_cutoff] + 'N' * end_pad
     mut_indices = [-1] * start_pad + mut_indices[start_cutoff:end_cutoff] + [-1] * end_pad
-    print(f"Mut and Ref are equal: {mut_seq == ref_seq}")
+    # print(f"Mut and Ref are equal: {mut_seq == ref_seq}")
 
     copy_mut_indices = mut_indices.copy()
 
@@ -1041,8 +1042,8 @@ 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)
-            print("RUNNING")
-            ref_transcript, var_transcript = Gene(mutation.mut_id.split(':')[0], organism='mm39').transcript(gene_data.transcript_id), Gene(mutation.mut_id.split(':')[0], variation=mutation.mut_id, organism='mm39').transcript(gene_data.transcript_id)
+            # print(f"RUNNING: {mutation.mut_id}")
+            ref_transcript, var_transcript = Gene(mutation.mut_id.split(':')[0], organism='mm39').transcript(gene_data.transcript_id), Gene(mutation.mut_id.split(':')[0], mutation.mut_id, organism='mm39').transcript(gene_data.transcript_id)
             print(f"Second check : {ref_transcript.pre_mrna == var_transcript.pre_mrna}")
             self.missplicing = find_transcript_missplicing(self.modification, ref_transcript, var_transcript, context=sai_mrg_context+min_coverage, threshold=threshold,
                                 engine=engine)

{geney-1.2.15.dist-info → geney-1.2.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.15
+Version: 1.2.17
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.15.dist-info → geney-1.2.17.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=c7OHbgPCDd1ouF3mckGQE-r15xgGJv9hMuabY7ApTMU,77965
+geney/oncosplice.py,sha256=Ram8jY69AxVspa13jN4eQD0iUX5dUuz9fXQzG3QoJl0,78052
 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-1.2.15.dist-info/METADATA,sha256=g6y36w6g8u5eT09QXz0_EEPGxLpVy0OCTLmGe91u2w4,1199
-geney-1.2.15.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-geney-1.2.15.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.15.dist-info/RECORD,,
+geney-1.2.17.dist-info/METADATA,sha256=-fToNRmK9zXLOqq-LRzgPHk8E0_d4ecgfukN35KHlso,1199
+geney-1.2.17.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+geney-1.2.17.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.17.dist-info/RECORD,,