def _get_allele_line(self, record, sample_fullname_list):
'''
'''
#line = [record.CHROM, record.POS, record.REF]
#alt_list = [alt.value for alt in record.ALT]
#line += [",".join(alt_list)]
line = list()
line += [
AlleleSelect.allele_convert(
"{}/{}".format(record.call_for_sample[fn].gt_alleles[0],
record.call_for_sample[fn].gt_alleles[1]),
"allele") for fn in sample_fullname_list
]
line_str = '\t'.join(map(str, line))
return line_str
def print_allele(self):
''' When show_genotype is specified, the genotype of the specified
regions and members are output to a file.
main
variant.py print_allele
allele_select.py cls allele_int
'''
proc_name = "genotype"
log.info("-------------------------------")
log.info("Start processing {}\n".format(proc_name))
# header
header = list()
header += ["CHROM", "POS", "Rlen", "Alen", "diff", "REF", "ALT"]
header += glv.conf.group_members_dict['all']
# reader
reader = vcfpy.Reader.from_path(glv.conf.vcf_file_path)
total_cnt = len(glv.conf.region_name_list)
# Save to file for each region
for proc_cnt, region_name in enumerate(glv.conf.region_name_list, 1):
region = glv.conf.regions_dict[region_name]['reg']
# Create a list of fullname for the specified members
sample_fullname_list = list()
for nickname in glv.conf.group_members_dict['all']:
sample_fullname_list.append(utl.get_fullname(nickname))
# if group priority
#sample_fullname_list = \
# utl.get_sample_list_from_groupname(
# group_list, "fullname")
# out file name
outf_pref = "005_genotype"
basename = "{}~{}~{}".format(outf_pref, region_name,
glv.conf.show_genotype)
out_file_path = "{}/{}.txt".format(glv.conf.out_dir_path, basename)
# backup
utl.save_to_tmpfile(out_file_path)
log.info("")
log.info("{} / {}, {}({}) > {}".format(proc_cnt, total_cnt,
region_name, region,
out_file_path))
start = time.time()
with open(out_file_path, mode='w') as f:
f.write("{}\n".format('\t'.join(map(str, header))))
vcf_ittr = reader.fetch(region)
for record in vcf_ittr:
# Main informations
line = [record.CHROM, record.POS]
alt_list = [alt.value for alt in record.ALT]
# variant length and diff
len_ref = len(record.REF)
lens_alt_list = list()
for alt in alt_list:
lens_alt_list.append(len(alt))
diff_len = abs(len_ref - lens_alt_list[0])
lens_alt = ",".join(map(str, lens_alt_list))
line += [len_ref]
line += [lens_alt]
line += [diff_len]
line += [record.REF]
line += [",".join(alt_list)]
line += [
AlleleSelect.allele_convert(
"{}/{}".format(
record.call_for_sample[fn].gt_alleles[0],
record.call_for_sample[fn].gt_alleles[1]),
glv.conf.show_genotype)
for fn in sample_fullname_list
]
f.write("{}\n".format('\t'.join(map(str, line))))
log.info("genotype {} > {}.txt\n".format(
utl.elapsed_time(time.time(), start), out_file_path))