Mercurial > repos > fubar > microsatbed
comparison find_str.py @ 26:26e9575c2c83 draft
planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty
| author | fubar |
|---|---|
| date | Fri, 19 Jul 2024 22:20:43 +0000 |
| parents | 8d0b8a75350f |
| children | efc775ab30fe |
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| 25:8d0b8a75350f | 26:26e9575c2c83 |
|---|---|
| 1 import argparse | 1 import argparse |
| 2 import shutil | 2 import shutil |
| 3 import subprocess | |
| 3 | 4 |
| 4 import pybigtools | 5 import pybigtools |
| 5 import pytrf # 1.3.0 | 6 import pytrf # 1.3.0 |
| 6 from pyfastx import Fastx # 0.5.2 | 7 from pyfastx import Fastx # 0.5.2 |
| 7 | 8 |
| 17 for b in bed: | 18 for b in bed: |
| 18 nt = b[5] | 19 nt = b[5] |
| 19 bin = int(b[1] / winwidth) | 20 bin = int(b[1] / winwidth) |
| 20 d[bin] += nt | 21 d[bin] += nt |
| 21 dw = [ | 22 dw = [ |
| 22 (name, (x * winwidth)+1, (x + 1) * winwidth, float(d[x])) | 23 (name, (x * winwidth), ((x + 1) * winwidth) - 1, float(d[x])) |
| 23 for x in range(nwin + 1) | 24 for x in range(nwin + 1) |
| 24 if (x + 1) * winwidth <= chrlen - 1 | 25 if (x + 1) * winwidth <= chrlen |
| 25 ] | 26 ] |
| 26 return dw | 27 return dw |
| 27 | 28 |
| 28 | 29 |
| 29 def write_ssrs(args): | 30 def write_ssrs(args): |
| 76 cbed.append(row) | 77 cbed.append(row) |
| 77 elif args.penta and len(ssr.motif) == 5: | 78 elif args.penta and len(ssr.motif) == 5: |
| 78 cbed.append(row) | 79 cbed.append(row) |
| 79 elif args.hexa and len(ssr.motif) == 6: | 80 elif args.hexa and len(ssr.motif) == 6: |
| 80 cbed.append(row) | 81 cbed.append(row) |
| 81 bed += cbed | |
| 82 if args.bigwig: | 82 if args.bigwig: |
| 83 w = getDensity(name, cbed, chrlen, args.winwidth) | 83 w = getDensity(name, cbed, chrlen, args.winwidth) |
| 84 wig += w | 84 wig += w |
| 85 bed += cbed | |
| 85 if args.bigwig: | 86 if args.bigwig: |
| 86 wig.sort() | 87 wig.sort() |
| 87 bw = pybigtools.open("temp.bw", "w") | 88 bedg = ['%s %d %d %.3f' % x for x in wig] |
| 88 bw.write(chrlens, wig) | 89 # bedg.insert(0,'track type=bedGraph') https://genomebrowser.wustl.edu/goldenPath/help/bigWig.html |
| 90 with open("temp.bedg", "w") as bw: | |
| 91 bw.write('\n'.join(bedg)) | |
| 92 chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()] | |
| 93 with open("temp.chromlen", "w") as cl: | |
| 94 cl.write('\n'.join(chroms)) | |
| 95 cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", "temp.bw" ] | |
| 96 subprocess.run(cmd) | |
| 97 #bw = pybigtools.open("temp.bw", "w") | |
| 98 #bw.write(chrlens, wig) | |
| 89 shutil.move("temp.bw", args.bed) | 99 shutil.move("temp.bw", args.bed) |
| 90 else: | 100 else: |
| 91 bed.sort() | 101 bed.sort() |
| 92 obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed] | 102 obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed] |
| 93 with open(args.bed, "w") as outbed: | 103 with open(args.bed, "w") as outbed: |