Read if contig is circurlar in gff attribute

labgem · Nov 28, 2023 · 33b249f · 33b249f
1 parent d8fcf91
commit 33b249f
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/ppanggolin/annotate/annotate.py b/ppanggolin/annotate/annotate.py
@@ -334,7 +334,8 @@ def get_id_attribute(attributes_dict: dict) -> str:
                 attributes = get_gff_attributes(fields_gff)
                 pseudogene = False
                 if fields_gff[gff_type] == 'region':
-                    if fields_gff[gff_seqname] in circular_contigs:
+                    if fields_gff[gff_seqname] in circular_contigs or ('Is_circular' in attributes and
+                                                                       attributes['Is_circular']):
                         contig.is_circular = True
                 elif fields_gff[gff_type] == 'CDS' or "RNA" in fields_gff[gff_type]:
                     gene_id = attributes.get("PROTEIN_ID")