Mercurial > repos > artbio > manta

comparison customConfigManta.py @ 5:f55d45b0c6d1 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
author artbio
date Tue, 09 Jun 2020 06:23:39 -0400
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4:d09254e37c68 5:f55d45b0c6d1
1 import argparse
2
3
4 def Parser():
5 the_parser = argparse.ArgumentParser()
6 the_parser.add_argument(
7 '--minCandidateVariantSize', type=int, default=8,
8 help="Run Manta reporting for all SVs/indels at or above this size")
9 the_parser.add_argument(
10 '--rnaMinCandidateVariantSize', type=int, default=1000,
11 help="Separate option (to provide different default) used for \
12 runs in RNA-mode")
13 the_parser.add_argument(
14 '--minEdgeObservations', type=int, default=3,
15 help="Remove all edges from the graph unless they're supported \
16 by this many 'observations'")
17 the_parser.add_argument(
18 '--graphNodeMaxEdgeCount', type=int, default=10,
19 help="If both nodes of an edge have an edge count higher than this, \
20 then skip evaluation of the edge")
21 the_parser.add_argument(
22 '--minCandidateSpanningCount', type=int, default=3,
23 help="Run discovery and candidate reporting for all SVs/indels with \
24 at least this many spanning support observations")
25 the_parser.add_argument(
26 '--minScoredVariantSize', type=int, default=50,
27 help="After candidate identification, only score and report \
28 SVs/indels at or above this size")
29 the_parser.add_argument(
30 '--minDiploidVariantScore', type=int, default=10,
31 help="minimum VCF QUAL score for a variant to be included in \
32 the diploid vcf")
33 the_parser.add_argument(
34 '--minPassDiploidVariantScore', type=int, default=20,
35 help="VCF QUAL score below which a variant is marked as \
36 filtered in the diploid vcf")
37 the_parser.add_argument(
38 '--minPassDiploidGTScore', type=int, default=15,
39 help="minimum genotype quality score below which single samples \
40 are filtered for a variant in the diploid vcf")
41 the_parser.add_argument(
42 '--minSomaticScore', type=int, default=10,
43 help="minimum VCF QUAL score for a variant to be included in the \
44 diploid vcf")
45 the_parser.add_argument(
46 '--minPassSomaticScore', type=int, default=30,
47 help="somatic quality scores below this level are filtered in the \
48 somatic vcf")
49 the_parser.add_argument(
50 '--enableRemoteReadRetrievalForInsertionsInGermlineCallingModes',
51 type=int, default=1,
52 help="includes tumor-normal subtraction and tumor-only calling")
53 the_parser.add_argument(
54 '--enableRemoteReadRetrievalForInsertionsInCancerCallingModes',
55 type=int, default=0,
56 help="GermlineCallingModes includes all other calling modes")
57 the_parser.add_argument(
58 '--useOverlapPairEvidence', type=int, default=0,
59 help="Set 1 if an overlapping read pair will be considered as \
60 evidence. Set to 0 to skip overlapping read pairs")
61 args = the_parser.parse_args()
62 return args
63
64
65 if __name__ == "__main__":
66 args = Parser()
67 # recover arguments as a dictionary with keys = argument name and values
68 # are argument values
69 argsDict = args.__dict__
70 ini_lines = []
71 # implement first, hard-coded ini lines
72 ini_lines.append('[manta]')
73 ini_lines.append('referenceFasta = /dummy/path/to/genome.fa')
74 # implement the rest of the ini lines for the argsDict
75 for argument in argsDict:
76 ini_lines.append("%s = %s" % (argument, str(argsDict[argument])))
77 # print ini_lines in configManta.py.ini
78 handler = open('configManta.py.ini', 'w')
79 for line in ini_lines:
80 handler.write("%s\n" % line)