diff cravat_convert/cravat_convert.py @ 21:67a13940d0bf draft default tip

Uploaded

--- a/cravat_convert/cravat_convert.py	Thu Aug 16 15:10:34 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-from __future__ import print_function
-import os
-import argparse
-from vcf_converter import CravatConverter
-
-def get_vcf_mapping():
-    """ : VCF Headers mapped to their index position in a row of VCF values.
-        : These are only the mandatory columns, per the VCF spec.
-    """
-    return {
-        'CHROM': 0,
-        'POS': 1,
-        'ID': 2,
-        'REF': 3,
-        'ALT': 4,
-        'QUAL': 5,
-        'FILTER': 6,
-        'INFO': 7
-    }
-
-
-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 = None,
-                            help = 'Output path to write the cravat file to')
-    return parser.parse_args()
-
-
-def convert(in_path, out_path=None, cr_sep='\t', cr_newline='\n'):
-    """ : Convert a VCF file to a Cravat file.
-        : Arguments:
-            : in_path: <str> path to input vcf file
-            : out_path: <str> path to output cravat file. Will defualt to cravat_converted.txt in the input directory.
-            : cr_sep: <str> the value delimiter for the output cravat file. Default value of '\\t'.
-            : out_newline: <str> the newline delimiter in the output cravat file. Default of '\\n'
-    """
-    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()
-        # A dictionary of mandatory vcf headers mapped to their row indices
-        vcf_mapping = get_vcf_mapping()
-
-        for line in in_file:
-            if line.startswith("#"):
-                continue
-            line = line.strip().split()
-            # 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()
-    if cli_args.output == None:
-        base, _ = os.path.split(cli_args.input)
-        cli_args.output = os.path.join(base, "cravat_converted.txt") 
-    convert(in_path = cli_args.input, out_path = cli_args.output)