filter_regions_non-autosomal_chr.py

# the COUNTS_FILE can come with or without non-autosomal chrs (e.g. chrX for female)
# by default, will make sure only autosomal are in; optionally keep ones listed in sys.argv[3:] (e.g. chrX again)

import sys

keep_chrs     = ['chr' + str(c) for c in range(1,23)] + [str(c) for c in range(1,23)]
if len(sys.argv) > 2: 
    keep_chrs = keep_chrs + ['chr' + c for c in sys.argv[2:]] + sys.argv[2:]

region_chr_dict = {}
with open(sys.argv[1],'r') as regionsf:
    for line in regionsf:
        chrm, _, _, region = line.strip().split('\t')
        region_chr_dict [region] = chrm      

#with open(sys.argv[2],'w') as rm_regions_f:
for line in sys.stdin:

    if not line.startswith('#'):
        region, hap1_count, hap2_count, hap1_allele_ratio, p_binom, snv_count, snv_hap1_hap2_coords, mmap_log = line.split('\t')

        if region_chr_dict[region] in keep_chrs: sys.stdout.write(line)
#        else: rm_regions_f.write('\t'.join([region, region_chr_dict[region]] + ['_chr_filter\n']))
    else: sys.stdout.write(line)