Mercurial > repos > fubar > microsatbed
changeset 24:94c5f834c0cc draft
planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty
| author | fubar |
|---|---|
| date | Fri, 19 Jul 2024 05:20:35 +0000 |
| parents | 45f690db0eaf |
| children | 8d0b8a75350f |
| files | find_str.py test-data/dibed_wig_sample test.bw |
| diffstat | 3 files changed, 25 insertions(+), 18 deletions(-) [+] |
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--- a/find_str.py Wed Jul 17 23:19:12 2024 +0000 +++ b/find_str.py Fri Jul 19 05:20:35 2024 +0000 @@ -2,7 +2,6 @@ import shutil import pybigtools - import pytrf # 1.3.0 from pyfastx import Fastx # 0.5.2 @@ -11,16 +10,22 @@ Designed to build some of the microsatellite tracks from https://github.com/arangrhie/T2T-Polish/tree/master/pattern for the VGP. """ + def getDensity(name, bed, chrlen, winwidth): - nwin = int(chrlen/winwidth) - d = [0.0 for x in range(nwin+1)] + nwin = int(chrlen / winwidth) + d = [0.0 for x in range(nwin + 1)] for b in bed: nt = b[5] - bin = int(b[1]/winwidth) + bin = int(b[1] / winwidth) d[bin] += nt - dw = [(name,x*winwidth,(x+1)*winwidth,float(d[x])) for x in range(nwin+1) if (x+1)*winwidth <= chrlen] + dw = [ + (name, (x * winwidth)+1, (x + 1) * winwidth, float(d[x])) + for x in range(nwin + 1) + if (x + 1) * winwidth <= chrlen + ] return dw + def write_ssrs(args): """ The integers in the call change the minimum repeats for mono-, di-, tri-, tetra-, penta-, hexa-nucleotide repeats @@ -39,15 +44,15 @@ for name, seq in fa: cbed = [] for ssr in pytrf.STRFinder( - name, - seq, - args.monomin, - args.dimin, - args.trimin, - args.tetramin, - args.pentamin, - args.hexamin, - ): + name, + seq, + args.monomin, + args.dimin, + args.trimin, + args.tetramin, + args.pentamin, + args.hexamin, + ): row = ( ssr.chrom, ssr.start, @@ -73,13 +78,15 @@ cbed.append(row) bed += cbed if args.bigwig: - chrlens[name] = len(seq) - w = getDensity(name, cbed, len(seq), args.winwidth) + chrlen = len(seq) + chrlens[name] = chrlen + w = getDensity(name, cbed, chrlen, args.winwidth) wig += w if args.bigwig: wig.sort() - bw = pybigtools.open("temp.bw", 'w') - bw.write(chrlens,wig) + bw = pybigtools.open("temp.bw", "w") + bw.write(chrlens, wig) + bw.close() shutil.move("temp.bw", args.bed) else: bed.sort()