Mercurial > repos > fubar > microsatbed
comparison find_str.py @ 25:8d0b8a75350f draft
planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty
| author | fubar |
|---|---|
| date | Fri, 19 Jul 2024 06:41:18 +0000 |
| parents | 94c5f834c0cc |
| children | 26e9575c2c83 |
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| 24:94c5f834c0cc | 25:8d0b8a75350f |
|---|---|
| 19 bin = int(b[1] / winwidth) | 19 bin = int(b[1] / winwidth) |
| 20 d[bin] += nt | 20 d[bin] += nt |
| 21 dw = [ | 21 dw = [ |
| 22 (name, (x * winwidth)+1, (x + 1) * winwidth, float(d[x])) | 22 (name, (x * winwidth)+1, (x + 1) * winwidth, float(d[x])) |
| 23 for x in range(nwin + 1) | 23 for x in range(nwin + 1) |
| 24 if (x + 1) * winwidth <= chrlen | 24 if (x + 1) * winwidth <= chrlen - 1 |
| 25 ] | 25 ] |
| 26 return dw | 26 return dw |
| 27 | 27 |
| 28 | 28 |
| 29 def write_ssrs(args): | 29 def write_ssrs(args): |
| 40 specific = None | 40 specific = None |
| 41 if args.specific: | 41 if args.specific: |
| 42 specific = args.specific.upper().split(",") | 42 specific = args.specific.upper().split(",") |
| 43 fa = Fastx(args.fasta, uppercase=True) | 43 fa = Fastx(args.fasta, uppercase=True) |
| 44 for name, seq in fa: | 44 for name, seq in fa: |
| 45 chrlen = len(seq) | |
| 46 chrlens[name] = chrlen | |
| 45 cbed = [] | 47 cbed = [] |
| 46 for ssr in pytrf.STRFinder( | 48 for ssr in pytrf.STRFinder( |
| 47 name, | 49 name, |
| 48 seq, | 50 seq, |
| 49 args.monomin, | 51 args.monomin, |
| 76 cbed.append(row) | 78 cbed.append(row) |
| 77 elif args.hexa and len(ssr.motif) == 6: | 79 elif args.hexa and len(ssr.motif) == 6: |
| 78 cbed.append(row) | 80 cbed.append(row) |
| 79 bed += cbed | 81 bed += cbed |
| 80 if args.bigwig: | 82 if args.bigwig: |
| 81 chrlen = len(seq) | |
| 82 chrlens[name] = chrlen | |
| 83 w = getDensity(name, cbed, chrlen, args.winwidth) | 83 w = getDensity(name, cbed, chrlen, args.winwidth) |
| 84 wig += w | 84 wig += w |
| 85 if args.bigwig: | 85 if args.bigwig: |
| 86 wig.sort() | 86 wig.sort() |
| 87 bw = pybigtools.open("temp.bw", "w") | 87 bw = pybigtools.open("temp.bw", "w") |
| 88 bw.write(chrlens, wig) | 88 bw.write(chrlens, wig) |
| 89 bw.close() | |
| 90 shutil.move("temp.bw", args.bed) | 89 shutil.move("temp.bw", args.bed) |
| 91 else: | 90 else: |
| 92 bed.sort() | 91 bed.sort() |
| 93 obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed] | 92 obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed] |
| 94 with open(args.bed, "w") as outbed: | 93 with open(args.bed, "w") as outbed: |