From d21e63f59e3c8055b1f6e89df07cd7ac4cf73f74 Mon Sep 17 00:00:00 2001
From: Matt Shirley <mdshw5@gmail.com>
Date: Thu, 2 Nov 2023 13:21:32 -0400
Subject: [PATCH] Skip transcripts with missing transcript_id tags

---
 pisces/index.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pisces/index.py b/pisces/index.py
index 69a5cf3..71c0ce2 100755
--- 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(