Mercurial > repos > iuc > variant_analyzer

annotate mut2sscs.py @ 2:18fcf8017300 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
author iuc
date Tue, 10 Nov 2020 12:54:49 +0000
parents 833d9e71b864
children
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5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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1 #!/usr/bin/env python
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3 """mut2sscs.py
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5 Author -- Gundula Povysil
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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6 Contact -- povysil@bioinf.jku.at
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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8 Takes a tabular file with mutations from DCS and a BAM file of SSCS as input
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9 and extracts all tags of reads that carry the mutation.
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10 Calculates statistics about number of ab/ba/duplex per mutation.
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12 ======= ========== ================= ================================
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13 Version Date Author Description
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18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
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14 2.0.0 2020-10-30 Gundula Povysil -
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15 ======= ========== ================= ================================
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17 USAGE: python mut2sscs.py DCS_Mutations.tabular SSCS.bam SSCS_counts.json
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19 """
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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21 from __future__ import division
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23 import argparse
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24 import json
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25 import os
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26 import sys
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28 import pysam
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29 from cyvcf2 import VCF
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32 def make_argparser():
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33 parser = argparse.ArgumentParser(description='Takes a vcf file with mutations and a BAM file as input and prints all tags of reads that carry the mutation to a user specified output file.')
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34 parser.add_argument('--mutFile',
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35 help='VCR file with DCS mutations.')
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36 parser.add_argument('--bamFile',
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37 help='BAM file with aligned SSCS reads.')
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38 parser.add_argument('--outputJson',
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39 help='Output JSON file to store SSCS counts.')
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40 return parser
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43 def mut2sscs(argv):
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44 parser = make_argparser()
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45 args = parser.parse_args(argv[1:])
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47 file1 = args.mutFile
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48 file2 = args.bamFile
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49 sscs_counts_json = args.outputJson
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51 if os.path.isfile(file1) is False:
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52 sys.exit("Error: Could not find '{}'".format(file1))
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54 if os.path.isfile(file2) is False:
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55 sys.exit("Error: Could not find '{}'".format(file2))
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56
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57 # read SSCS bam file
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58 bam = pysam.AlignmentFile(file2, "rb")
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60 # get tags
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61 mut_pos_dict = {}
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62 ref_pos_dict = {}
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63
2
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64 for variant in VCF(file1):
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65 chrom = variant.CHROM
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66 stop_pos = variant.start
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67 chrom_stop_pos = str(chrom) + "#" + str(stop_pos)
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68 ref = variant.REF
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69 alt = variant.ALT[0]
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70
2
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71 if len(ref) == len(alt):
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72 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=1000000000):
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73 if pileupcolumn.reference_pos == stop_pos:
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74 count_alt = 0
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75 count_ref = 0
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76 count_indel = 0
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77 print("unfiltered reads=", pileupcolumn.n, "filtered reads=", len(pileupcolumn.pileups),
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78 "difference= ", len(pileupcolumn.pileups) - pileupcolumn.n)
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79 for pileupread in pileupcolumn.pileups:
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80 if not pileupread.is_del and not pileupread.is_refskip:
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81 tag = pileupread.alignment.query_name
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82 abba = tag[-2:]
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83 # query position is None if is_del or is_refskip is set.
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parents: 1
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84 if pileupread.alignment.query_sequence[pileupread.query_position] == alt:
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
85 count_alt += 1
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
86 if chrom_stop_pos in mut_pos_dict:
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
87 if abba in mut_pos_dict[chrom_stop_pos]:
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
88 mut_pos_dict[chrom_stop_pos][abba] += 1
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
89 else:
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
90 mut_pos_dict[chrom_stop_pos][abba] = 1
0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
91 else:
2
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
92 mut_pos_dict[chrom_stop_pos] = {}
0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
93 mut_pos_dict[chrom_stop_pos][abba] = 1
2
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
94 if chrom_stop_pos not in ref_pos_dict:
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
95 ref_pos_dict[chrom_stop_pos] = {}
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
96 ref_pos_dict[chrom_stop_pos][abba] = 0
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
97
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
98 elif pileupread.alignment.query_sequence[pileupread.query_position] == ref:
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
99 count_ref += 1
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
100 if chrom_stop_pos in ref_pos_dict:
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
101 if abba in ref_pos_dict[chrom_stop_pos]:
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
102 ref_pos_dict[chrom_stop_pos][abba] += 1
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
103 else:
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
104 ref_pos_dict[chrom_stop_pos][abba] = 1
0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
105 else:
2
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
106 ref_pos_dict[chrom_stop_pos] = {}
0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
107 ref_pos_dict[chrom_stop_pos][abba] = 1
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
108 else:
2
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
109 count_indel += 1
0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
110
2
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
111 print("coverage at pos %s = %s, ref = %s, alt = %s, indel = %s,\n" %
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
112 (pileupcolumn.pos, count_ref + count_alt, count_ref, count_alt, count_indel))
0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
113
2
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
114 # if mutation is in DCS file but not in SSCS, then set counts to NA
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
115 if chrom_stop_pos not in mut_pos_dict.keys():
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
116 mut_pos_dict[chrom_stop_pos] = {}
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
117 mut_pos_dict[chrom_stop_pos]["ab"] = 0
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
118 mut_pos_dict[chrom_stop_pos]["ba"] = 0
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
119 ref_pos_dict[chrom_stop_pos] = {}
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
120 ref_pos_dict[chrom_stop_pos]["ab"] = 0
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
121 ref_pos_dict[chrom_stop_pos]["ba"] = 0
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
122 else:
18fcf8017300 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
iuc
parents: 1
diff changeset
123 print("indels are currently not evaluated")
0
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
124 bam.close()
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
125
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
126 # save counts
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
127 with open(sscs_counts_json, "w") as f:
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
128 json.dump((mut_pos_dict, ref_pos_dict), f)
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
129
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
130
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
131 if __name__ == '__main__':
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff changeset
132 sys.exit(mut2sscs(sys.argv))