Mercurial > repos > in_silico > cravat_score_and_annotate
diff cravat_convert/cravat_convert.py @ 21:67a13940d0bf draft default tip
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author | in_silico |
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date | Thu, 16 Aug 2018 15:10:43 -0400 |
parents | 6da9a12f04b5 |
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--- 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)