Mercurial > repos > fubar > microsatbed
view find_str.py @ 6:43d5f89e508c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
author | fubar |
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date | Sat, 13 Jul 2024 12:54:13 +0000 |
parents | 1085e094cf5f |
children | ee773bbde3c3 |
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import argparse import pytrf # 1.3.0 from pyfastx import Fastx # 0.5.2 """ Allows all STR or those for a subset of motifs to be written to a bed file Designed to build some of the microsatellite tracks from https://github.com/arangrhie/T2T-Polish/tree/master/pattern for the VGP. """ def write_ssrs(args): """ The integers in the call change the minimum repeats for mono-, di-, tri-, tetra-, penta-, hexa-nucleotide repeats ssrs = pytrf.STRFinder(name, seq, 10, 6, 4, 3, 3, 3) NOTE: Dinucleotides GA and AG are reported separately by https://github.com/marbl/seqrequester. The reversed pair STRs are about as common in the documentation sample. Sequence read bias might be influenced by GC density or some other specific motif. """ bed = [] specific = None if args.specific: specific = args.specific.upper().split(",") fa = Fastx(args.fasta, uppercase=True) for name, seq in fa: if args.specific: ssrs = pytrf.STRFinder( name, seq, args.minreps, args.minreps, args.minreps, args.minreps, args.minreps, args.minreps, ) else: ssrs = pytrf.STRFinder( name, seq, args.monomin, args.dimin, args.trimin, args.tetramin, args.pentamin, args.hexamin, ) for ssr in ssrs: row = ( ssr.chrom, ssr.start - 1, ssr.end, ssr.motif, ssr.repeat, 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: bed.append(row) elif args.mono and len(ssr.motif) == 1: bed.append(row) elif args.di and len(ssr.motif) == 2: bed.append(row) elif args.tri and len(ssr.motif) == 3: bed.append(row) elif args.tetra and len(ssr.motif) == 4: bed.append(row) elif args.penta and len(ssr.motif) == 5: bed.append(row) elif args.hexa and len(ssr.motif) == 6: bed.append(row) bed.sort() obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed] with open(args.bed, "w") as outbed: outbed.write("\n".join(obed)) outbed.write("\n") if __name__ == "__main__": parser = argparse.ArgumentParser() a = parser.add_argument a("--di", action="store_true") a("--tri", action="store_true") a("--tetra", action="store_true") a("--penta", action="store_true") a("--hexa", action="store_true") a("--mono", action="store_true") a("--dimin", default=2, type=int) a("--trimin", default=2, type=int) a("--tetramin", default=2, type=int) a("--pentamin", default=2, type=int) a("--hexamin", default=2, type=int) a("--monomin", default=2, type=int) a("-f", "--fasta", default="humsamp.fa") a("-b", "--bed", default="humsamp.bed") a("--specific", default=None) a("--minreps", default=2, type=int) args = parser.parse_args() write_ssrs(args)