python_scan.py

"""
A python version of the perl scan file
As the VCF is being parsed as .txt, Perl isn't mega useful so I'm back to py
"""

import os, sys

# This is the VCF file of results passed via clinical filtering script
input_file = sys.argv[1]
# The gene files will all be text, one gene symbol per line
gene_files = sys.argv[2:]
vcf_gene_dict = {}

with open(input_file, 'r') as handle:
    first_line = True
    for row in handle:
        if first_line:
            first_line = False
        # Alternative condition to allow Dup/Del results through
        #elif row == '':
        elif row == '' or 'ablation' in row or 'amplification' in row:
            continue
        else:
            genes = row.split('\t')[5].split(',')
            for gene in genes:
                if gene in vcf_gene_dict:
                    vcf_gene_dict[gene].add(row)
                else:
                    vcf_gene_dict[gene] = set([(row)])
if '' in vcf_gene_dict.keys(): del vcf_gene_dict['']
if '.' in vcf_gene_dict.keys(): del vcf_gene_dict['.']

for filename in gene_files:
    with open(filename, 'r') as handle:
        print '----------{}'.format(filename)
        for gene in handle:
            gene = gene.rstrip()
            if gene in vcf_gene_dict:
                for row in vcf_gene_dict[gene]:
                    print row.rstrip()