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)