Mercurial > repos > dfornika > ivar_variants_to_vcf

comparison ivar_variants_to_vcf.py @ 0:c87f6ad32fd8 draft default tip

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"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
author dfornika
date Fri, 05 Jun 2020 05:10:05 +0000
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-1:000000000000 0:c87f6ad32fd8
1 #!/usr/bin/env python
2 import os
3 import sys
4 import re
5 import errno
6 import argparse
7
8 def parse_args(args=None):
9 Description = 'Convert iVar variants tsv file to vcf format.'
10 Epilog = """Example usage: python ivar_variants_to_vcf.py <FILE_IN> <FILE_OUT>"""
11
12 parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
13 parser.add_argument('FILE_IN', help="Input tsv file.")
14 parser.add_argument('FILE_OUT', help="Full path to output vcf file.")
15 parser.add_argument('-po', '--pass_only', dest="PASS_ONLY", help="Only output variants that PASS all filters.",action='store_true')
16 parser.add_argument('-ma', '--min_allele_freq', type=float, dest="MIN_ALLELE_FREQ", default=0, help="Only output variants where allele frequency greater than this number (default: 0).")
17
18 return parser.parse_args(args)
19
20 def make_dir(path):
21 if not len(path) == 0:
22 try:
23 os.makedirs(path)
24 except OSError as exception:
25 if exception.errno != errno.EEXIST:
26 raise
27
28 def ivar_variants_to_vcf(FileIn,FileOut,passOnly=False,minAF=0):
29 filename = os.path.splitext(FileIn)[0]
30 header = ('##fileformat=VCFv4.2\n'
31 '##source=iVar\n'
32 '##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n'
33 '##FILTER=<ID=PASS,Description="Result of p-value <= 0.05">\n'
34 '##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">\n'
35 '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n'
36 '##FORMAT=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base">\n'
37 '##FORMAT=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads">\n'
38 '##FORMAT=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base">\n'
39 '##FORMAT=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base">\n'
40 '##FORMAT=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads">\n'
41 '##FORMAT=<ID=ALT_QUAL,Number=1,Type=String,Description="Mean quality of alternate base">\n'
42 '##FORMAT=<ID=ALT_FREQ,Number=1,Type=String,Description="Frequency of alternate base">\n')
43 header += '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t'+filename+'\n'
44
45 varList = []
46 varCountDict = {'SNP':0, 'INS':0, 'DEL':0}
47 OutDir = os.path.dirname(FileOut)
48 make_dir(OutDir)
49 fout = open(FileOut,'w')
50 fout.write(header)
51 with open(FileIn) as f:
52 for line in f:
53 if not re.match("REGION",line):
54 line = re.split("\t", line)
55 CHROM=line[0]
56 POS=line[1]
57 ID='.'
58 REF=line[2]
59 ALT=line[3]
60 var_type = 'SNP'
61 if ALT[0] == '+':
62 ALT = REF + ALT[1:]
63 var_type = 'INS'
64 elif ALT[0] == '-':
65 REF += ALT[1:]
66 ALT = line[2]
67 var_type = 'DEL'
68 QUAL='.'
69 pass_test=line[13]
70 if pass_test == 'TRUE':
71 FILTER='PASS'
72 else:
73 FILTER='FAIL'
74 INFO='DP='+line[11]
75 FORMAT='GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ'
76 SAMPLE='1:'+line[4]+':'+line[5]+':'+line[6]+':'+line[7]+':'+line[8]+':'+line[9]+':'+line[10]
77 oline = CHROM+'\t'+POS+'\t'+ID+'\t'+REF+'\t'+ALT+'\t'+QUAL+'\t'+FILTER+'\t'+INFO+'\t'+FORMAT+'\t'+SAMPLE+'\n'
78 writeLine = True
79 if passOnly and FILTER != 'PASS':
80 writeLine = False
81 if float(line[10]) < minAF:
82 writeLine = False
83 if (CHROM,POS,REF,ALT) in varList:
84 writeLine = False
85 else:
86 varList.append((CHROM,POS,REF,ALT))
87 if writeLine:
88 varCountDict[var_type] += 1
89 fout.write(oline)
90 fout.close()
91
92 ## Print variant counts to pass to MultiQC
93 varCountList = [(k, str(v)) for k, v in sorted(varCountDict.items())]
94 print('\t'.join(['sample'] + [x[0] for x in varCountList]))
95 print('\t'.join([filename] + [x[1] for x in varCountList]))
96
97 def main(args=None):
98 args = parse_args(args)
99 ivar_variants_to_vcf(args.FILE_IN,args.FILE_OUT,args.PASS_ONLY,args.MIN_ALLELE_FREQ)
100
101
102 if __name__ == '__main__':
103 sys.exit(main())