default=im.examples.CHR22 + '/hutt.tfam',
help='Pedigree file to read genotyped subject IDs from (e.g., 1415 Hutterites)')
parser.add_option('-d', '--delimiter', type='str' , dest='delimiter', default='\\t',
help='Delimiter [default: %default. Use the string ''\t'' for a tab]')
parser.add_option('-t', '--override-tag', type='int' , dest='override_tag',
default=im.constants.UNPHASED, help='Tag value to tag overridden genotypes with')
parser.add_option('-w', '--warnings', action='store_true' , dest='warnings', default=False,
help='Print warning information about allele coding flipping but does not flip coding in output')
parser.add_option('-k', '--key', type='str' , dest='key', default='bp',
help='Key column to use in matching imputed and plink rows. ''bp'': \
match on base-pair position. ''name'': match on SNP name. Name MUST BE NUMERIC. \
Suitable for PLINK files generated from CGI files, where name is the CGI variant ID \
and uniquely identifies the SNP whereas the base-pair position does not.')
options, args = parser.parse_args(sys.argv[1:])
if len(args) != 2:
print usage
sys.exit(1)
if options.delimiter == '\\t': options.delimiter = '\t'
return args, options
if __name__ == '__main__':
'''Main program - accepts CLI arguments.'''
try:
args, options = __parse_command_line_args()
overridden_lines = __override_imputed_by_plink(args[1], args[0], options)
# Write overridden lines to standard output
util.write_buffered_lines(overridden_lines, sys.stdout, buf_size=options.buf_size, delimiter=options.delimiter)
except (IOError, OSError):
traceback.print_exc(file=sys.stdout)
sys.exit(141)
': \
match on base-pair position. '
'name'
': match on SNP name. Name MUST BE NUMERIC. \
Suitable for PLINK files generated from CGI files, where name is the CGI variant ID \
and uniquely identifies the SNP whereas the base-pair position does not.'
)
options, args = parser.parse_args(sys.argv[1:])
if len(args) != 2:
print usage
sys.exit(1)
if options.delimiter == '\\t': options.delimiter = '\t'
return args, options
if __name__ == '__main__':
'''Main program - accepts CLI arguments.'''
try:
args, options = __parse_command_line_args()
overridden_lines = __override_imputed_by_plink(args[1], args[0],
options)
# Write overridden lines to standard output
util.write_buffered_lines(overridden_lines,
sys.stdout,
buf_size=options.buf_size,
delimiter=options.delimiter,
process_line_factory=process_line_factory)
except (IOError, OSError):
traceback.print_exc(file=sys.stdout)
sys.exit(141)
default=im.examples.CHR22 + '/hutt.tfam',
help='Pedigree file to read genotyped subject IDs from (e.g., 1415 Hutterites)')
parser.add_option('-d', '--delimiter', type='str' , dest='delimiter', default='\\t',
help='Delimiter [default: %default. Use the string ''\t'' for a tab]')
parser.add_option('-t', '--override-tag', type='int' , dest='override_tag',
default=im.constants.UNPHASED, help='Tag value to tag overridden genotypes with')
parser.add_option('-w', '--warnings', action='store_true' , dest='warnings', default=False,
help='Print warning information about allele coding flipping but does not flip coding in output')
parser.add_option('-k', '--key', type='str' , dest='key', default='bp',
help='Key column to use in matching imputed and plink rows. ''bp'': \
match on base-pair position. ''name'': match on SNP name. Name MUST BE NUMERIC. \
Suitable for PLINK files generated from CGI files, where name is the CGI variant ID \
and uniquely identifies the SNP whereas the base-pair position does not.')
options, args = parser.parse_args(sys.argv[1:])
if len(args) != 2:
print usage
sys.exit(1)
if options.delimiter == '\\t': options.delimiter = '\t'
return args, options
if __name__ == '__main__':
'''Main program - accepts CLI arguments.'''
try:
args, options = __parse_command_line_args()
overridden_lines = __override_imputed_by_plink(args[1], args[0], options)
# Write overridden lines to standard output
util.write_buffered_lines(overridden_lines, sys.stdout, buf_size=options.buf_size, delimiter=options.delimiter, process_line_factory=process_line_factory)
except (IOError, OSError):
traceback.print_exc(file=sys.stdout)
sys.exit(141)
'bp'
': \
match on base-pair position. '
'name'
': match on SNP name. Name MUST BE NUMERIC. \
Suitable for PLINK files generated from CGI files, where name is the CGI variant ID \
and uniquely identifies the SNP whereas the base-pair position does not.'
)
options, args = parser.parse_args(sys.argv[1:])
if len(args) != 2:
print usage
sys.exit(1)
if options.delimiter == '\\t': options.delimiter = '\t'
return args, options
if __name__ == '__main__':
'''Main program - accepts CLI arguments.'''
try:
args, options = __parse_command_line_args()
overridden_lines = __override_imputed_by_plink(args[1], args[0],
options)
# Write overridden lines to standard output
util.write_buffered_lines(overridden_lines,
sys.stdout,
buf_size=options.buf_size,
delimiter=options.delimiter)
except (IOError, OSError):
traceback.print_exc(file=sys.stdout)
sys.exit(141)
