--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ivar_variants_to_vcf.py	Fri Jun 05 05:10:05 2020 +0000
@@ -0,0 +1,103 @@
+#!/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('-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).")
+
+    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.MIN_ALLELE_FREQ)
+
+
+if __name__ == '__main__':
+    sys.exit(main())