From 8ffc75f16e1d6ef44a3771b3d1fc4b475aaf700d Mon Sep 17 00:00:00 2001 From: "Timothy R. Fallon, PhD" Date: Mon, 8 Apr 2024 07:18:47 -0700 Subject: [PATCH] Update funannotate-p2g.py for contig_expand to use int --- funannotate/aux_scripts/funannotate-p2g.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/funannotate/aux_scripts/funannotate-p2g.py b/funannotate/aux_scripts/funannotate-p2g.py index c248b89..1123345 100755 --- a/funannotate/aux_scripts/funannotate-p2g.py +++ b/funannotate/aux_scripts/funannotate-p2g.py @@ -33,7 +33,7 @@ def __init__(self, prog): help='Final exonerate output file') parser.add_argument('-t', '--tblastn_out', help='Save tblastn output') parser.add_argument('--maxintron', default=3000, help='Maximum intron size') -parser.add_argument('--contig_expand', default=3000, help='number of basepairs to expand from tblastn/diamond alignments, to allow exonerate to find the target despite imprecise alignments') +parser.add_argument('--contig_expand', default=3000, type=int, help='number of basepairs to expand from tblastn/diamond alignments, to allow exonerate to find the target despite imprecise alignments') parser.add_argument('--exonerate_pident', default=80, help='Exonerate pct identity') parser.add_argument('--logfile', default='funannotate-p2g.log', help='logfile')