Grab GTF tags from exons

Novartis · Nov 17, 2021 · 14d0c22 · 14d0c22
1 parent 0218188
commit 14d0c22
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/pisces/index.py b/pisces/index.py
@@ -297,17 +297,17 @@ def features_to_string(features, fasta_in, masked=True, strand=True):
                                 total=db.count_features_of_type('gene'),
                                 unit='gene') as pbar:
                             for gene in db.features_of_type('gene'):
-                                first_transcript = next(
+                                first_exon = next(
                                     db.children(
                                         gene,
-                                        featuretype='transcript',
+                                        featuretype='exon',
                                         order_by='start'))
                                 try:
                                     if options["gene_type"] == True:
                                         type_tag = "gene_type"
                                     else:
                                         type_tag = options["gene_type"]
-                                    gene_type = first_transcript[type_tag][0]
+                                    gene_type = first_exon[type_tag][0]
                                 except KeyError:
                                     logging.info("No gene type tag found for %s", gene['gene_id'][0])
                                     gene_type = 'NA'
@@ -316,7 +316,7 @@ def features_to_string(features, fasta_in, masked=True, strand=True):
                                         name_tag = "gene_name"
                                     else:
                                         name_tag = options["gene_name"]
-                                    gene_name = first_transcript[name_tag][0]
+                                    gene_name = first_exon[name_tag][0]
                                 except KeyError:
                                     logging.info("No gene name tag found for %s", gene['gene_id'][0])
                                     gene_name = 'NA'