I think we have a first working version for further testing

scripts/stringtie2utr.py

@@ -1,5 +1,19 @@
 #!/usr/bin/env python3
 
+"""
+Script Name: stringtie2utr.py
+Description: This script decorates a gtf file with genes generated by AUGUSTUS,
+             BRAKER, or TSEBRA, which UTR features from a stringtie gtf file.
+Author: Katharina J. Hoff
+Email: [email protected]
+Date: September 29th 2023
+
+Copyright (C) The year of copyright, Katharina J. Hoff, University of Greifswald
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the Artistic License.
+"""
+
 import argparse
 import re
 from intervaltree import IntervalTree, Interval
@@ -450,9 +464,10 @@ def print_gtf(gtf_dict, gene_dict, tx_to_gene_dict, tx_dict):
     printed_gene = {}
     # Iterate over gene_dict entries
     for tx_id, tx_line in tx_dict.items():
-        if not tx_id in printed_gene:
+        gene_id = tx_to_gene_dict[tx_id]
+        if not gene_id in printed_gene:
             print(gene_dict[tx_to_gene_dict[tx_id]])
-            gene_printed = True
+            printed_gene[gene_id] = True
         print(tx_line)
         sorted_features = sorted(gtf_dict.get(tx_id, []), key=lambda x: int(x.split('\t')[3]))
         for feature in sorted_features:
@@ -463,7 +478,6 @@ def print_gtf(gtf_dict, gene_dict, tx_to_gene_dict, tx_dict):
                 # build new gtf line
                 print(fields[0] + "\tstringtie2utr\t", "\t".join(fields[2:8]), "\ttranscript_id \"" + tx_id + "\"; gene_id \"" + tx_to_gene_dict[tx_id] + "\";")
             else:
-            #elif "StringTie" not in feature:
                 print(feature)
 
 def build_tree(data):
@@ -669,8 +683,5 @@ def main():
     # print the updated tsebra_gtf
     print_gtf(tsebra_gtf, tsebra_gene_line_dict, tsebra_tx_to_gene_dict, tsebra_tx_dict)
 
-
-    print(overlaps)
-
 if __name__ == "__main__":
     main()