--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ivar_variants_to_vcf.py	Thu Jun 10 22:05:18 2021 +0000
@@ -0,0 +1,158 @@
+#!/usr/bin/env python
+import argparse
+import errno
+import os
+import re
+import sys
+
+
+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",
+    )
+
+    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 info_line(info_keys, kv):
+    info_strings = []
+    for key in info_keys:
+        if key not in kv:
+            raise KeyError(
+                'Expected key {} missing from INFO field key value pairs'
+                .format(key)
+            )
+        if kv[key] is False:
+            # a FLAG element, which should not be set
+            continue
+        if kv[key] is True:
+            # a FLAG element => write the key only
+            info_strings.append(key)
+        else:
+            info_strings.append('{}={}'.format(key, kv[key]))
+    return ';'.join(info_strings)
+
+
+def ivar_variants_to_vcf(FileIn, FileOut, passOnly=False):
+    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'
+        '##INFO=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base">\n'
+        '##INFO=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads">\n'
+        '##INFO=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base">\n'
+        '##INFO=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base">\n'
+        '##INFO=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads">\n'
+        '##INFO=<ID=ALT_QUAL,Number=1,Type=Integer,Description="Mean quality of alternate base">\n'
+        '##INFO=<ID=AF,Number=1,Type=Float,Description="Frequency of alternate base">\n'
+        '##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n'
+        '##FILTER=<ID=PASS,Description="Result of p-value <= 0.05">\n'
+        '##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">\n'
+    )
+    info_keys = [
+        re.match(r'##INFO=<ID=([^,]+),', line).group(1)
+        for line in header.splitlines()
+        if line.startswith('##INFO=')
+    ]
+    header += (
+        "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"
+    )
+
+    vars_seen = set()
+    varCountDict = {"SNP": 0, "INS": 0, "DEL": 0}
+    OutDir = os.path.dirname(FileOut)
+    make_dir(OutDir)
+    with open(FileIn) as f, open(FileOut, "w") as fout:
+        fout.write(header)
+        for line in f:
+            if line.startswith("REGION"):
+                continue
+
+            line = line.split("\t")
+            CHROM = line[0]
+            POS = line[1]
+            ID = "."
+            REF = line[2]
+            ALT = line[3]
+            if ALT[0] == "+":
+                ALT = REF + ALT[1:]
+                var_type = "INS"
+            elif ALT[0] == "-":
+                REF += ALT[1:]
+                ALT = line[2]
+                var_type = "DEL"
+            else:
+                var_type = "SNP"
+            QUAL = "."
+            pass_test = line[13]
+            if pass_test == "TRUE":
+                FILTER = "PASS"
+            else:
+                FILTER = "FAIL"
+
+            if (passOnly and FILTER != "PASS"):
+                continue
+            var = (CHROM, POS, REF, ALT)
+            if var in vars_seen:
+                continue
+
+            info_elements = {
+                'DP': line[11],
+                'REF_DP': line[4],
+                'REF_RV': line[5],
+                'REF_QUAL': line[6],
+                'ALT_DP': line[7],
+                'ALT_RV': line[8],
+                'ALT_QUAL': line[9],
+                'AF': line[10]
+            }
+            if var_type in ['INS', 'DEL']:
+                # add INDEL FLAG
+                info_elements['INDEL'] = True
+            else:
+                info_elements['INDEL'] = False
+            INFO = info_line(info_keys, info_elements)
+
+            vars_seen.add(var)
+            varCountDict[var_type] += 1
+            fout.write(
+                '\t'.join(
+                    [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO]
+                ) + '\n'
+            )
+
+    # 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
+    )
+
+
+if __name__ == "__main__":
+    sys.exit(main())