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annotate customConfigManta.py @ 6:cb5691381acb draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 01bc6749826f5ef4a22540a9aa6a5ffd93786d4c
author artbio
date Thu, 08 Jun 2023 17:36:38 +0000
parents f55d45b0c6d1
children
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f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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1 import argparse
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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2
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3
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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4 def Parser():
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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5 the_parser = argparse.ArgumentParser()
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6 the_parser.add_argument(
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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7 '--minCandidateVariantSize', type=int, default=8,
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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8 help="Run Manta reporting for all SVs/indels at or above this size")
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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9 the_parser.add_argument(
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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10 '--rnaMinCandidateVariantSize', type=int, default=1000,
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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11 help="Separate option (to provide different default) used for \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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12 runs in RNA-mode")
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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13 the_parser.add_argument(
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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14 '--minEdgeObservations', type=int, default=3,
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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15 help="Remove all edges from the graph unless they're supported \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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16 by this many 'observations'")
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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17 the_parser.add_argument(
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18 '--graphNodeMaxEdgeCount', type=int, default=10,
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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19 help="If both nodes of an edge have an edge count higher than this, \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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20 then skip evaluation of the edge")
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21 the_parser.add_argument(
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22 '--minCandidateSpanningCount', type=int, default=3,
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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23 help="Run discovery and candidate reporting for all SVs/indels with \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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24 at least this many spanning support observations")
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25 the_parser.add_argument(
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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26 '--minScoredVariantSize', type=int, default=50,
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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27 help="After candidate identification, only score and report \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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28 SVs/indels at or above this size")
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29 the_parser.add_argument(
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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30 '--minDiploidVariantScore', type=int, default=10,
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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31 help="minimum VCF QUAL score for a variant to be included in \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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32 the diploid vcf")
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33 the_parser.add_argument(
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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34 '--minPassDiploidVariantScore', type=int, default=20,
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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35 help="VCF QUAL score below which a variant is marked as \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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36 filtered in the diploid vcf")
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37 the_parser.add_argument(
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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38 '--minPassDiploidGTScore', type=int, default=15,
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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39 help="minimum genotype quality score below which single samples \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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40 are filtered for a variant in the diploid vcf")
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41 the_parser.add_argument(
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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42 '--minSomaticScore', type=int, default=10,
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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43 help="minimum VCF QUAL score for a variant to be included in the \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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44 diploid vcf")
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45 the_parser.add_argument(
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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46 '--minPassSomaticScore', type=int, default=30,
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47 help="somatic quality scores below this level are filtered in the \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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48 somatic vcf")
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49 the_parser.add_argument(
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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50 '--enableRemoteReadRetrievalForInsertionsInGermlineCallingModes',
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51 type=int, default=1,
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52 help="includes tumor-normal subtraction and tumor-only calling")
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53 the_parser.add_argument(
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54 '--enableRemoteReadRetrievalForInsertionsInCancerCallingModes',
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55 type=int, default=0,
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56 help="GermlineCallingModes includes all other calling modes")
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57 the_parser.add_argument(
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58 '--useOverlapPairEvidence', type=int, default=0,
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59 help="Set 1 if an overlapping read pair will be considered as \
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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60 evidence. Set to 0 to skip overlapping read pairs")
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61 args = the_parser.parse_args()
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62 return args
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63
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64
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65 if __name__ == "__main__":
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66 args = Parser()
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67 # recover arguments as a dictionary with keys = argument name and values
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68 # are argument values
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69 argsDict = args.__dict__
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70 ini_lines = []
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71 # implement first, hard-coded ini lines
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72 ini_lines.append('[manta]')
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73 ini_lines.append('referenceFasta = /dummy/path/to/genome.fa')
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74 # implement the rest of the ini lines for the argsDict
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75 for argument in argsDict:
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76 ini_lines.append("%s = %s" % (argument, str(argsDict[argument])))
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77 # print ini_lines in configManta.py.ini
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78 handler = open('configManta.py.ini', 'w')
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79 for line in ini_lines:
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80 handler.write("%s\n" % line)