parser = argparse.ArgumentParser(description=( 'Given FASTA on stdin, write the ids, sequences, and ' 'quality strings on a single TAB-separated line to stdout.')) parser.add_argument('--separator', default='\t', help=('The character string to separate ids from ' 'sequences and quality strings (if any)')) parser.add_argument('--removeIds', default=False, action='store_true', help='Do not print sequence ids') addFASTACommandLineOptions(parser) args = parser.parse_args() sep = args.separator reads = parseFASTACommandLineOptions(args) # Duplicate code a little so as not to repeatedly do two tests per read. if args.fastq: if args.removeIds: for read in reads: print(read.sequence + sep + read.quality) else: for read in reads: print(read.id + sep + read.sequence + sep + read.quality) else: if args.removeIds: for read in reads:
if __name__ == '__main__': import argparse parser = argparse.ArgumentParser( description=( 'Given FASTA on stdin, write the ids, sequences, and ' 'quality strings on a single TAB-separated line to stdout.')) parser.add_argument('--separator', default='\t', help=('The character string to separate ids from ' 'sequences and quality strings (if any)')) parser.add_argument('--removeIds', default=False, action='store_true', help='Do not print sequence ids') addFASTACommandLineOptions(parser) args = parser.parse_args() sep = args.separator reads = parseFASTACommandLineOptions(args) # Duplicate code a little so as not to repeatedly do two tests for read. if args.fastq: if args.removeIds: for read in reads: print(read.sequence + sep + read.quality) else: for read in reads: print(read.id + sep + read.sequence + sep + read.quality) else: if args.removeIds: for read in reads: