Mercurial > repos > iuc > ivar_consensus

comparison ivar_variants_to_vcf.py @ 6:3bc2ef3d4a17 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
author iuc
date Thu, 10 Jun 2021 22:07:43 +0000
parents
children 17f911830a8c
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5:5e668dc9f379 6:3bc2ef3d4a17
1 #!/usr/bin/env python
2 import argparse
3 import errno
4 import os
5 import re
6 import sys
7
8
9 def parse_args(args=None):
10 Description = "Convert iVar variants tsv file to vcf format."
11 Epilog = """Example usage: python ivar_variants_to_vcf.py <FILE_IN> <FILE_OUT>"""
12
13 parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
14 parser.add_argument("FILE_IN", help="Input tsv file.")
15 parser.add_argument("FILE_OUT", help="Full path to output vcf file.")
16 parser.add_argument(
17 "-po",
18 "--pass_only",
19 dest="PASS_ONLY",
20 help="Only output variants that PASS all filters.",
21 action="store_true",
22 )
23
24 return parser.parse_args(args)
25
26
27 def make_dir(path):
28 if not len(path) == 0:
29 try:
30 os.makedirs(path)
31 except OSError as exception:
32 if exception.errno != errno.EEXIST:
33 raise
34
35
36 def info_line(info_keys, kv):
37 info_strings = []
38 for key in info_keys:
39 if key not in kv:
40 raise KeyError(
41 'Expected key {} missing from INFO field key value pairs'
42 .format(key)
43 )
44 if kv[key] is False:
45 # a FLAG element, which should not be set
46 continue
47 if kv[key] is True:
48 # a FLAG element => write the key only
49 info_strings.append(key)
50 else:
51 info_strings.append('{}={}'.format(key, kv[key]))
52 return ';'.join(info_strings)
53
54
55 def ivar_variants_to_vcf(FileIn, FileOut, passOnly=False):
56 filename = os.path.splitext(FileIn)[0]
57 header = (
58 "##fileformat=VCFv4.2\n"
59 "##source=iVar\n"
60 '##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n'
61 '##INFO=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base">\n'
62 '##INFO=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads">\n'
63 '##INFO=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base">\n'
64 '##INFO=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base">\n'
65 '##INFO=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads">\n'
66 '##INFO=<ID=ALT_QUAL,Number=1,Type=Integer,Description="Mean quality of alternate base">\n'
67 '##INFO=<ID=AF,Number=1,Type=Float,Description="Frequency of alternate base">\n'
68 '##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n'
69 '##FILTER=<ID=PASS,Description="Result of p-value <= 0.05">\n'
70 '##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">\n'
71 )
72 info_keys = [
73 re.match(r'##INFO=<ID=([^,]+),', line).group(1)
74 for line in header.splitlines()
75 if line.startswith('##INFO=')
76 ]
77 header += (
78 "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"
79 )
80
81 vars_seen = set()
82 varCountDict = {"SNP": 0, "INS": 0, "DEL": 0}
83 OutDir = os.path.dirname(FileOut)
84 make_dir(OutDir)
85 with open(FileIn) as f, open(FileOut, "w") as fout:
86 fout.write(header)
87 for line in f:
88 if line.startswith("REGION"):
89 continue
90
91 line = line.split("\t")
92 CHROM = line[0]
93 POS = line[1]
94 ID = "."
95 REF = line[2]
96 ALT = line[3]
97 if ALT[0] == "+":
98 ALT = REF + ALT[1:]
99 var_type = "INS"
100 elif ALT[0] == "-":
101 REF += ALT[1:]
102 ALT = line[2]
103 var_type = "DEL"
104 else:
105 var_type = "SNP"
106 QUAL = "."
107 pass_test = line[13]
108 if pass_test == "TRUE":
109 FILTER = "PASS"
110 else:
111 FILTER = "FAIL"
112
113 if (passOnly and FILTER != "PASS"):
114 continue
115 var = (CHROM, POS, REF, ALT)
116 if var in vars_seen:
117 continue
118
119 info_elements = {
120 'DP': line[11],
121 'REF_DP': line[4],
122 'REF_RV': line[5],
123 'REF_QUAL': line[6],
124 'ALT_DP': line[7],
125 'ALT_RV': line[8],
126 'ALT_QUAL': line[9],
127 'AF': line[10]
128 }
129 if var_type in ['INS', 'DEL']:
130 # add INDEL FLAG
131 info_elements['INDEL'] = True
132 else:
133 info_elements['INDEL'] = False
134 INFO = info_line(info_keys, info_elements)
135
136 vars_seen.add(var)
137 varCountDict[var_type] += 1
138 fout.write(
139 '\t'.join(
140 [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO]
141 ) + '\n'
142 )
143
144 # Print variant counts to pass to MultiQC
145 varCountList = [(k, str(v)) for k, v in sorted(varCountDict.items())]
146 print("\t".join(["sample"] + [x[0] for x in varCountList]))
147 print("\t".join([filename] + [x[1] for x in varCountList]))
148
149
150 def main(args=None):
151 args = parse_args(args)
152 ivar_variants_to_vcf(
153 args.FILE_IN, args.FILE_OUT, args.PASS_ONLY
154 )
155
156
157 if __name__ == "__main__":
158 sys.exit(main())