From 24a43b9d137cc0d210f6a98ed526b3cc63d66e7e Mon Sep 17 00:00:00 2001 From: Oliver Schwengers Date: Mon, 4 Dec 2023 17:03:41 +0100 Subject: [PATCH] obey seq completeness provided in replicons file --- bakta/utils.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/bakta/utils.py b/bakta/utils.py index b5b229b7..c458d616 100644 --- a/bakta/utils.py +++ b/bakta/utils.py @@ -456,10 +456,9 @@ def qc_contigs(contigs: Sequence[dict], replicons: Dict[str, dict]) -> Tuple[Seq if(replicon): contig['type'] = replicon['replicon_type'] contig['topology'] = replicon['topology'] + contig['complete'] = replicon['replicon_type'] != bc.REPLICON_CONTIG if(replicon['name']): contig['name'] = replicon['name'] - if(replicon['replicon_type'] != bc.REPLICON_CONTIG): - contig['complete'] = True if(not cfg.keep_contig_headers): contig['orig_id'] = contig['id'] contig['id'] = replicon['new_locus_id'] if replicon['new_locus_id'] else contig['simple_id']