Mercurial > repos > artbio > lumpy_smoove

comparison vcf2hrdetect.py @ 9:7dcf61950215 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 5f62b58c65917afbb018296568c81ad132106012
author artbio
date Wed, 05 Apr 2023 15:56:13 +0000
parents ad8853ee9909
children
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8:b4dec06d8fc6 9:7dcf61950215
24 else: 24 else:
25 tabdict[newid] = [vcfdict[id][0], vcfdict[id][1], 25 tabdict[newid] = [vcfdict[id][0], vcfdict[id][1],
26 chrom, coordbreak, "TRA"] 26 chrom, coordbreak, "TRA"]
27 for id in list(vcfdict): 27 for id in list(vcfdict):
28 if "_" in id: 28 if "_" in id:
29 del(vcfdict[id]) 29 del vcfdict[id]
30 for id in vcfdict.keys(): # only sv that are not of type TRA or INV 30 for id in vcfdict.keys(): # only sv that are not of type TRA or INV
31 chr1 = vcfdict[id][0] 31 chr1 = vcfdict[id][0]
32 chr2 = vcfdict[id][0] 32 chr2 = vcfdict[id][0]
33 pos1 = vcfdict[id][1] 33 pos1 = vcfdict[id][1]
34 pos2 = vcfdict[id][7].split("END=")[1].split(";")[0] 34 pos2 = vcfdict[id][7].split("END=")[1].split(";")[0]