Skip transcripts with missing transcript_id tags

Novartis · Nov 2, 2023 · d21e63f · d21e63f
1 parent 4cd66d6
commit d21e63f
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/pisces/index.py b/pisces/index.py
@@ -339,6 +339,10 @@ def features_to_string(features, fasta_in, masked=True, strand=True):
                                 transcripts = tuple(db.children(gene, featuretype='transcript', order_by='start'))
                                 if len(transcripts) == 0:  # gene that has no transcripts
                                     continue  # gene will have no transcript sequence or exons
+                                try:
+                                    transcript['transcript_id']
+                                except KeyError:
+                                    continue  # transcript id is missing (ex TRNAV-CAC gene in RefSeq)
                                 for transcript in transcripts:
                                     # Write entry in the transcripts to genes table
                                     gene2tx.write("{txp}\t{gene}\n".format(