filter_non-autosomal_chr.py

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) > 1: 
    keep_chrs = keep_chrs + ['chr' + c for c in sys.argv[1:]] + sys.argv[1:]

#with open(sys.argv[1],'a') as rm_hetSNV_f:
for line in sys.stdin:

    if not line.startswith('#'):
        (chrm,ref_coord,hap1_coord,hap2_coord,ref_allele,hap1_allele,hap2_allele,
                 cA,cC,cG,cT,cN,ref_allele_ratio,sum_ref_n_alt_cnts,p_binom,
                 cnv, mmap_log) = line.split('\t')

        if chrm in keep_chrs: sys.stdout.write(line)
#        else: rm_hetSNV_f.write('\t'.join([chrm,ref_coord, 
#               '_'.join([cA,cC,cG,cT,'','chr_filter'])])+'\n')
    else: sys.stdout.write(line)