ivar_variants_to_vcf.py

#!/usr/bin/env python
import os
import sys
import re
import errno
import argparse

def parse_args(args=None):
    Description = 'Convert iVar variants tsv file to vcf format.'
    Epilog = """Example usage: python ivar_variants_to_vcf.py <FILE_IN> <FILE_OUT>"""

    parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
    parser.add_argument('FILE_IN', help="Input tsv file.")
    parser.add_argument('FILE_OUT', help="Full path to output vcf file.")
    parser.add_argument('-po', '--pass_only', dest="PASS_ONLY", help="Only output variants that PASS all filters.",action='store_true')
    parser.add_argument('-af', '--allele_freq_thresh', type=float, dest="ALLELE_FREQ_THRESH", default=0, help="Only output variants where allele frequency greater than this number (default: 0).")

    return parser.parse_args(args)

def make_dir(path):
    if not len(path) == 0:
        try:
            os.makedirs(path)
        except OSError as exception:
            if exception.errno != errno.EEXIST:
                raise

def ivar_variants_to_vcf(FileIn,FileOut,passOnly=False,minAF=0):
    filename = os.path.splitext(FileIn)[0]
    header = ('##fileformat=VCFv4.2\n'
              '##source=iVar\n'
              '##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n'
              '##FILTER=<ID=PASS,Description="Result of p-value <= 0.05">\n'
              '##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">\n'
              '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n'
              '##FORMAT=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base">\n'
              '##FORMAT=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads">\n'
              '##FORMAT=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base">\n'
              '##FORMAT=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base">\n'
              '##FORMAT=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads">\n'
              '##FORMAT=<ID=ALT_QUAL,Number=1,Type=String,Description="Mean quality of alternate base">\n'
              '##FORMAT=<ID=ALT_FREQ,Number=1,Type=String,Description="Frequency of alternate base">\n')
    header += '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t'+filename+'\n'

    varList = []
    varCountDict = {'SNP':0, 'INS':0, 'DEL':0}
    OutDir = os.path.dirname(FileOut)
    make_dir(OutDir)
    fout = open(FileOut,'w')
    fout.write(header)
    with open(FileIn) as f:
        for line in f:
            if not re.match("REGION",line):
                line = re.split("\t", line)
                CHROM=line[0]
                POS=line[1]
                ID='.'
                REF=line[2]
                ALT=line[3]
                var_type = 'SNP'
                if ALT[0] == '+':
                    ALT = REF + ALT[1:]
                    var_type = 'INS'
                elif ALT[0] == '-':
                    REF += ALT[1:]
                    ALT = line[2]
                    var_type = 'DEL'
                QUAL='.'
                pass_test=line[13]
                if pass_test == 'TRUE':
                    FILTER='PASS'
                else:
                    FILTER='FAIL'
                INFO='DP='+line[11]
                FORMAT='GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ'
                SAMPLE='1:'+line[4]+':'+line[5]+':'+line[6]+':'+line[7]+':'+line[8]+':'+line[9]+':'+line[10]
                oline = CHROM+'\t'+POS+'\t'+ID+'\t'+REF+'\t'+ALT+'\t'+QUAL+'\t'+FILTER+'\t'+INFO+'\t'+FORMAT+'\t'+SAMPLE+'\n'
                writeLine = True
                if passOnly and FILTER != 'PASS':
                    writeLine = False
                if float(line[10]) < minAF:
                    writeLine = False
                if (CHROM,POS,REF,ALT) in varList:
                    writeLine = False
                else:
                    varList.append((CHROM,POS,REF,ALT))
                if writeLine:
                    varCountDict[var_type] += 1
                    fout.write(oline)
    fout.close()

    ## Print variant counts to pass to MultiQC
    varCountList = [(k, str(v)) for k, v in sorted(varCountDict.items())]
    print('\t'.join(['sample'] + [x[0] for x in varCountList]))
    print('\t'.join([filename] + [x[1] for x in varCountList]))

def main(args=None):
    args = parse_args(args)
    ivar_variants_to_vcf(args.FILE_IN,args.FILE_OUT,args.PASS_ONLY,args.ALLELE_FREQ_THRESH)


if __name__ == '__main__':
    sys.exit(main())