# HG changeset patch # User fubar # Date 1721192880 0 # Node ID ee773bbde3c3d498b56c79fa88baae8d3085b634 # Parent 4af0486b85138fdb713ec8deac4d248ca0b0fb23 planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty diff -r 4af0486b8513 -r ee773bbde3c3 find_str.py --- a/find_str.py Wed Jul 17 04:28:28 2024 +0000 +++ b/find_str.py Wed Jul 17 05:08:00 2024 +0000 @@ -27,12 +27,12 @@ ssrs = pytrf.STRFinder( name, seq, - args.minreps, - args.minreps, - args.minreps, - args.minreps, - args.minreps, - args.minreps, + 2, + 1, + 2, + 2, + 2, + 2, ) else: ssrs = pytrf.STRFinder( @@ -55,7 +55,7 @@ ssr.length, ) # pytrf reports a 1 based start position so start-1 fixes the bed interval lengths - if args.specific and ssr.motif in specific: + if args.specific and ssr.motif in specific and ssr.repeat >= args.minreps: bed.append(row) elif args.mono and len(ssr.motif) == 1: bed.append(row) diff -r 4af0486b8513 -r ee773bbde3c3 microsatbed.xml --- a/microsatbed.xml Wed Jul 17 04:28:28 2024 +0000 +++ b/microsatbed.xml Wed Jul 17 05:08:00 2024 +0000 @@ -1,4 +1,4 @@ - + Short Tandem Repeats to bed features from fasta python