Mercurial > repos > fubar > microsatbed

comparison find_str.py @ 30:53c4f91c6031 draft default tip

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planemo upload for repository https://github.com/fubar2/microsatbed commit 80a8c0db54b6e2cab9dfe7178b1e5b3b39592f2c
author fubar
date Sat, 20 Jul 2024 01:44:09 +0000
parents efc775ab30fe
children
comparison
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29:efc775ab30fe 30:53c4f91c6031
86 w = getDensity(name, cbed, chrlen, args.winwidth) 86 w = getDensity(name, cbed, chrlen, args.winwidth)
87 wig += w 87 wig += w
88 bed += cbed 88 bed += cbed
89 if args.bigwig: 89 if args.bigwig:
90 wig.sort() 90 wig.sort()
91 bedg = ['%s %d %d %.3f' % x for x in wig] 91 bedg = ["%s %d %d %.3f" % x for x in wig]
92 with open("temp.bedg", "w") as bw: 92 with open("temp.bedg", "w") as bw:
93 bw.write('\n'.join(bedg)) 93 bw.write("\n".join(bedg))
94 chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()] 94 chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()]
95 with open("temp.chromlen", "w") as cl: 95 with open("temp.chromlen", "w") as cl:
96 cl.write('\n'.join(chroms)) 96 cl.write("\n".join(chroms))
97 cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", "temp.bw" ] 97 cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", "temp.bw"]
98 subprocess.run(cmd) 98 subprocess.run(cmd)
99 shutil.move("temp.bw", args.bed) 99 shutil.move("temp.bw", args.bed)
100 else: 100 else:
101 bed.sort() 101 bed.sort()
102 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]