Mercurial > repos > artbio > lumpy_smoove

annotate vcf2hrdetect.py @ 4:41704ce96c7f draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
author artbio
date Sun, 18 Apr 2021 17:07:32 +0000
parents
children 0dc7ea74bf61
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
1 import sys
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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2
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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3 handle = open(sys.argv[1], 'r')
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
4 vcfdict = dict()
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
5 tabdict = dict()
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
6 for line in handle:
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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7 if line[0] == "#":
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
8 continue
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
9 else:
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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10 tabline = line[:-1].split("\t")
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
11 vcfdict[tabline[2]] = tabline
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
12 for id in vcfdict.keys():
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
13 if "_1" in id:
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
14 newid = id[:-2]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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15 pointbreak = vcfdict[id][4]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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16 if "]" in pointbreak:
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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17 coordbreak = pointbreak.split("]")[1].split(":")[1]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
18 chrom = pointbreak.split("]")[1].split(":")[0]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
19 elif "[" in pointbreak:
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
20 coordbreak = pointbreak.split("[")[1].split(":")[1]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
21 chrom = pointbreak.split("[")[1].split(":")[0]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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22 if vcfdict[id][0] == chrom:
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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23 tabdict[newid] = [chrom, vcfdict[id][1], chrom, coordbreak, "INV"]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
24 else:
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
25 tabdict[newid] = [vcfdict[id][0], vcfdict[id][1],
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
26 chrom, coordbreak, "TRA"]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
27 for id in list(vcfdict):
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
28 if "_" in id:
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
29 del(vcfdict[id])
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
30 for id in vcfdict.keys(): # only sv that are not of type TRA or INV
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
31 chr1 = vcfdict[id][0]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
32 chr2 = vcfdict[id][0]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
33 pos1 = vcfdict[id][1]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
34 pos2 = vcfdict[id][7].split("END=")[1].split(";")[0]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
35 type = vcfdict[id][7].split("SVTYPE=")[1].split(";")[0]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
36 tabdict[id] = [chr1, pos1, chr2, pos2, type]
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
37 out = open(sys.argv[2], 'w')
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
38 out.write("chr1\tpos1\tchr2\tpos2\ttype\n")
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
39 for key in tabdict:
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
40 line = "\t".join(tabdict[key]) + "\n"
41704ce96c7f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
artbio
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diff changeset
41 out.write(line)