def filter_call(sample):
if mglobals.original:
os.chdir(join(mglobals.original_path, sample))
else:
os.chdir(join(mglobals.alternate_path, sample))
log.info("Filtering {0} by coverage".format(sample))
helpers.filter_vcf_by_coverage_cutoffs(vcf=(sample + in_file_extension), cutoff_table=mglobals.coverage_cutoffs)
log.info("Filtering {0} according to SNP file: {1}".format(sample, mglobals.current_snp_file))
dgrp_intersect_command = [
"nice",
"-n",
"5",
"intersectBed",
"-a",
(sample + "_covfil.vcf"), # the output of the helper
# function above.
"-b",
mglobals.current_snp_file,
"-wa",
]
sample_dgrp_intersect = sample + out_file_extension
with open(sample_dgrp_intersect, "w") as out:
helpers.sub_call(dgrp_intersect_command, stdout=out)
def filter_call(sample):
if mglobals.original:
os.chdir(join(mglobals.original_path, sample))
else:
os.chdir(join(mglobals.alternate_path, sample))
log.info('Filtering {0} by coverage'.format(sample))
helpers.filter_vcf_by_coverage_cutoffs(
vcf=(sample + in_file_extension),
cutoff_table=mglobals.coverage_cutoffs)
log.info('Filtering {0} according to SNP file: {1}'.format(
sample, mglobals.current_snp_file))
dgrp_intersect_command = [
'nice',
'-n',
'5',
'intersectBed',
'-a',
(sample + '_covfil.vcf'), # the output of the helper
# function above.
'-b',
mglobals.current_snp_file,
'-wa'
]
sample_dgrp_intersect = sample + out_file_extension
with open(sample_dgrp_intersect, 'w') as out:
helpers.sub_call(dgrp_intersect_command, stdout=out)
def filter_call(sample):
if mglobals.original:
os.chdir(join(mglobals.original_path, sample))
else:
os.chdir(join(mglobals.alternate_path, sample))
log.info('Filtering {0} by coverage'.format(sample))
helpers.filter_vcf_by_coverage_cutoffs(vcf=(sample + in_file_extension),
cutoff_table=mglobals.coverage_cutoffs)
os.rename((sample + '_covfil.vcf'), (sample + out_file_extension))
def filter_call(sample):
if mglobals.original:
os.chdir(join(mglobals.original_path, sample))
else:
os.chdir(join(mglobals.alternate_path, sample))
log.info('Filtering {0} by coverage'.format(sample))
helpers.filter_vcf_by_coverage_cutoffs(vcf=(sample + in_file_extension),
cutoff_table=mglobals.coverage_cutoffs)
log.info('Filtering {0} according to SNP file: {1}'.format(sample, mglobals.current_snp_file))
dgrp_intersect_command = ['nice', '-n', '5',
'intersectBed',
'-a', (sample + '_covfil.vcf'), # the output of the helper
# function above.
'-b', mglobals.current_snp_file,
'-wa'
]
sample_dgrp_intersect = sample + out_file_extension
with open(sample_dgrp_intersect, 'w') as out:
helpers.sub_call(dgrp_intersect_command, stdout=out)
