annotate cravat_convert/cravat_convert.py @ 20:6da9a12f04b5 draft

Uploaded

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)