Merge ccae7fa into 1b3fa5f

griffithlab · Oct 14, 2020 · 91d2047 · 91d2047
2 parents 1b3fa5f + ccae7fa
commit 91d2047
Showing 1 changed file with 9 additions and 11 deletions.
diff --git a/lib/proximal_variant.py b/lib/proximal_variant.py
@@ -100,22 +100,20 @@ def find_phased_somatic_variant_and_potential_proximal_variants(self, somatic_va
                         print("Warning: Proximal variant does not contain any VEP annotations for alternate allele and will be skipped: {}".format(entry))
                         continue
 
-                #We assume that there is only one CSQ entry because the PICK option was used but we should double check that
-                if len(csq_entries) > 1:
-                    print("Warning: There are multiple CSQ entries (consequences) for proximal variant {} and alternate allele {}. Using the first one.".format(entry, proximal_alt))
-
-                csq_entry = csq_entries[0]
+                picked_csq_entry = None
+                for csq_entry in csq_entries:
+                    if csq_entry['Feature'] == transcript:
+                        picked_csq_entry = csq_entry
+                if picked_csq_entry is None:
+                    print("Warning: Proximal variant has no transcript annotation for somatic variant of interest transcript {} and will be skipped: {}".format(transcript, entry))
+                    continue
 
-                consequences = {consequence.lower() for consequence in csq_entry['Consequence'].split('&')}
+                consequences = {consequence.lower() for consequence in picked_csq_entry['Consequence'].split('&')}
                 if 'missense_variant' not in consequences:
                     print("Warning: Proximal variant is not a missense mutation and will be skipped: {}".format(entry))
                     continue
 
-                if csq_entry['Feature'] != transcript:
-                    print("Warning: Proximal variant transcript is not the same as the somatic variant transcript. Proximal variant will be skipped: {}".format(entry))
-                    continue
-
-                potential_proximal_variants.append([entry, csq_entry])
+                potential_proximal_variants.append([entry, picked_csq_entry])
 
         return (phased_somatic_variant, potential_proximal_variants)