def processGenome(genomefile,
plinkexe,
bedprefix,
prefix,
nosex=False,
verbose=False,
threads=-1):
"""
Read the genome file (as produced by plink option --genome) and removes
one of the individuals that have over 0.05 pi_hat (%5 inbreeding coeff.)
:param str genomefile: filename of the genome
:param str plinkexe: Path and executable of plink
:param str bedprefix: Prefix for the bed fileset
:param str prefix: Prefix for the outputs
"""
if not threads:
threads = -1
if verbose:
print(' Processing %s file' % (genomefile))
gen = pd.read_table(genomefile,
delim_whitespace=True,
iterator=True,
chunksize=10000)
rels = Parallel(n_jobs=int(threads))(delayed(prcgenthreads)(ch)
for ch in gen)
rels = pd.concat(rels)
excludefile = '%s_relateds.toexclude' % (prefix)
rels.drop_duplicates().to_csv(excludefile,
sep=' ',
header=False,
index=False)
if verbose:
print('\t %d Individuals excluded as relative of other individuals' %
(rels.shape[1]))
plremov = (
'%s --bfile %s --remove %s_relateds.toexclude --make-bed --keep-'
'allele-oder --out %s')
if nosex:
plremov += ' --allow-no-sex'
plremov = plremov % (plinkexe, bedprefix, prefix, prefix)
if verbose:
print(' Removing individuals from file %s' % (excludefile))
execline(plremov)
