annotate cravat_convert/cravat_convert.py @ 1:152cc8feff8a draft

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'''
Convert a VCF format file to Cravat format file
'''

import os
import argparse
from vcf_converter import CravatConverter
###
import ipdb


# 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)