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:
