def pipeline_validation_experiment(location_file, true_type, true_location, pedigree, debug=False, remove_partial_calls=False):
'''Load (the ''true'') genotypes from an external source. Load a list of locations from ''location_file''. Impute them and compare
with the true genotypes.'''
g = extract_genotypes(location_file)
t = ImputationSet(pedigree, g)
if true_type == 'iplex': true_genotype = im.imputation.reader.iplex_to_genotype(true_location, t) # os.environ['OBER'] + '/data/impute/rare/to_livne_20121205', t)
else: raise ValueError('Unsupported true genotype format ''%s''' % (true_type,))
problem = Problem(pedigree, true_genotype)
p, t = impute_problem(problem, debug=debug, remove_partial_calls=remove_partial_calls)
return p, t
def pipeline_validation_experiment(
location_file, true_type, true_location, pedigree, debug=False, remove_partial_calls=False
):
"""Load (the ''true'') genotypes from an external source. Load a list of locations from ''location_file''. Impute them and compare
with the true genotypes."""
g = extract_genotypes(location_file)
t = ImputationSet(pedigree, g)
if true_type == "iplex":
true_genotype = im.imputation.reader.iplex_to_genotype(
true_location, t
) # os.environ['OBER'] + '/data/impute/rare/to_livne_20121205', t)
else:
raise ValueError("Unsupported true genotype format " "%s" "" % (true_type,))
problem = Problem(pedigree, true_genotype)
p, t = impute_problem(problem, debug=debug, remove_partial_calls=remove_partial_calls)
return p, t
help='Print debugging information')
parser.add_option('-n', '--no-swap-major-minor' , action='store_true' , dest='allele_swap', default=False,
help='Do not swap major/minor allele encoding based on the data') # Note: reads the no-allele-swap flag and then negates it below!
parser.add_option('-k', '--custom-identifier' , action='store_true' , dest='custom_id', default=False,
help='Assign custom identifiers to ALL snps, not just those with blank identifiers in the data')
options, args = parser.parse_args(sys.argv[1:])
options.allele_swap = not options.allele_swap
if not options.format in ['plink', 'npz']:
print 'Unreocgnized format ''%s''. Supported formats: plink, npz' % (options.format,)
print usage
if len(args) != 2:
print usage
sys.exit(1)
try:
input_file = sys.stdin if args[0] == '-' else open(args[0], 'rb')
g = extract_genotypes(input_file, index_file=options.index_file, var_file_prefix=options.var_file_prefix,
allele_swap=options.allele_swap, custom_id=options.custom_id, debug=options.debug)
out = args[1]
if options.format == 'npz':
im.io_genotype.write(options.format, g, out + '.npz')
elif options.format == 'plink':
# Does not yet include the genetic map . TODO: save it to a separate PLINK file if a dedicated
# PLINK format exists for this data
im.io_genotype.write(options.format, g, open(out + '.tped', 'wb'),
sample_id_out=out + '.tfam', recode_cgi=options.recode_cgi)
else:
raise ValueError('Unsupported output format ''%s''' % (options.format,))
except:
traceback.print_exc(file=sys.stdout)
sys.exit(util.EXIT_FAILURE)
'Assign custom identifiers to ALL snps, not just those with blank identifiers in the data'
)
options, args = parser.parse_args(sys.argv[1:])
options.allele_swap = not options.allele_swap
if not options.format in ['plink', 'npz']:
print 'Unreocgnized format ' '%s' '. Supported formats: plink, npz' % (
options.format, )
print usage
if len(args) != 2:
print usage
sys.exit(1)
try:
input_file = sys.stdin if args[0] == '-' else open(args[0], 'rb')
g = extract_genotypes(input_file,
index_file=options.index_file,
var_file_prefix=options.var_file_prefix,
allele_swap=options.allele_swap,
custom_id=options.custom_id,
debug=options.debug)
out = args[1]
if options.format == 'npz':
im.io_genotype.write(options.format, g, out + '.npz')
elif options.format == 'plink':
# Does not yet include the genetic map . TODO: save it to a separate PLINK file if a dedicated
# PLINK format exists for this data
im.io_genotype.write(options.format,
g,
open(out + '.tped', 'wb'),
sample_id_out=out + '.tfam',
recode_cgi=options.recode_cgi)
else:
raise ValueError('Unsupported output format '
