--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_convert/cravat_convert.py	Tue Jun 12 11:27:06 2018 -0400
@@ -0,0 +1,77 @@
+'''
+Convert a VCF format file to Cravat format file
+'''
+
+import os
+import argparse
+from vcf_converter import CravatConverter
+
+# File read/write configuration variables
+vcf_sep = '\t'
+cr_sep = '\t'
+cr_newline = '\n'
+
+# VCF Headers mapped to their index position in a row of VCF values
+vcf_mapping = {
+    'CHROM': 0,
+    'POS': 1,
+    'ID': 2,
+    'REF': 3,
+    'ALT': 4,
+    'QUAL': 5,
+    'FILTER': 6,
+    'INFO': 7,
+    'FORMAT': 8,
+    'NA00001': 9,
+    'NA00002': 10,
+    'NA00003': 11
+}
+
+
+def get_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input',
+                            '-i',
+                            required = True,
+                            help='Input path to a VCF file for conversion',)
+    parser.add_argument('--output',
+                            '-o',
+                            default = os.path.join(os.getcwd(), "cravat_converted.txt"),
+                            help = 'Output path to write the cravat file to')
+    return parser.parse_args()
+
+
+def convert(in_path, out_path=None):
+    if not out_path:
+        base, _ = os.path.split(in_path)
+        out_path = os.path.join(base, "cravat_converted.txt")
+    
+    with open(in_path, 'r') as in_file, \
+    open(out_path, 'w') as out_file:
+
+        # cr_count will be used to generate the 'TR' field of the cravat rows (first header)
+        cr_count = 0
+        # VCF lines are always assumed to be '+' strand, as VCF doesn't specify that attribute
+        strand = '+'
+        # VCF converter. Adjusts position, reference, and alternate for Cravat formatting.
+        converter = CravatConverter()
+
+        for line in in_file:
+            if line.startswith("#"):
+                continue
+            line = line.strip().split(vcf_sep)
+            # row is dict of VCF headers mapped to corresponding values of this line
+            row = { header: line[index] for header, index in vcf_mapping.items() }
+            for alt in row["ALT"].split(","):
+                new_pos, new_ref, new_alt = converter.extract_vcf_variant(strand, row["POS"], row["REF"], alt)
+                new_pos, new_ref, new_alt = str(new_pos), str(new_ref), str(new_alt)
+                cr_line = cr_sep.join([
+                    'TR' + str(cr_count), row['CHROM'], new_pos, strand, new_ref, new_alt, row['ID']
+                ])
+                out_file.write(cr_line + cr_newline)
+                cr_count += 1
+
+
+if __name__ == "__main__":
+    cli_args = get_args()
+    convert(cli_args.input, cli_args.output)