Add files via upload

PSI-Sigma_gff2gtf.py

@@ -0,0 +1,52 @@
+import argparse
+
+def gff_to_gtf(gff_filename, gtf_filename):
+    with open(gff_filename, 'r') as gff_file, open(gtf_filename, 'w') as gtf_file:
+        for line in gff_file:
+            if line.startswith('#') or line.strip() == '':
+                continue
+
+            fields = line.strip().split('\t')
+            attributes = fields[8]
+
+            # Extract ID, Name, and Parent if available
+            attr_dict = {attr.split('=')[0]: attr.split('=')[1] for attr in attributes.split(';') if '=' in attr}
+            gene_id = attr_dict.get('ID', '')
+            gene_name = attr_dict.get('Name', '')
+            transcript_id = attr_dict.get('Parent', '')
+
+            # Change 'mRNA' feature type to 'transcript' for GTF
+            feature_type = fields[2]
+            if feature_type == 'mRNA':
+                feature_type = 'transcript'
+
+            # Construct GTF attribute field
+            gtf_attributes = []
+            if feature_type == 'gene':
+                gtf_attributes.append(f'gene_id "{gene_id}"')
+                gtf_attributes.append(f'gene_name "{gene_name}"')
+            elif feature_type == 'transcript':
+                gtf_attributes.append(f'gene_id "{transcript_id}"')
+                gtf_attributes.append(f'transcript_id "{gene_id}"')
+            else: # exon or CDS
+                gtf_attributes.append(f'gene_id "{transcript_id.split(".")[0]}"')
+                gtf_attributes.append(f'transcript_id "{transcript_id}"')
+                exon_number = gene_id.split(".")[-1].lstrip('exon')
+                gtf_attributes.append(f'exon_number "{exon_number}"')
+                if feature_type == 'exon':
+                    gtf_attributes.append('transcript_biotype "unknown"')
+
+            gtf_attributes_str = '; '.join(gtf_attributes) + ';'
+            gtf_line = '\t'.join(fields[:2] + [feature_type] + fields[3:8]) + '\t' + gtf_attributes_str + '\n'
+            gtf_file.write(gtf_line)
+
+def main():
+    parser = argparse.ArgumentParser(description="Convert GFF file to GTF format.")
+    parser.add_argument("--gff", required=True, help="Input GFF file")
+    parser.add_argument("--gtf", required=True, help="Output GTF file")
+    args = parser.parse_args()
+
+    gff_to_gtf(args.gff, args.gtf)
+
+if __name__ == "__main__":
+    main()