def parse_arguments(debug=False):
parser = argparse.ArgumentParser(prog='ENCODE DCC fastq merger.',
description='')
parser.add_argument('fastqs',
nargs='+',
type=str,
help='TSV file path or list of FASTQs. '
'FASTQs must be compressed with gzip (with .gz). '
'Use TSV for multiple fastqs to be merged later. '
'row=merge_id, col=end_id).')
parser.add_argument('--paired-end',
action="store_true",
help='Paired-end FASTQs.')
parser.add_argument('--nth',
type=int,
default=1,
help='Number of threads to parallelize.')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
# parse fastqs command line
if args.fastqs[0].endswith('.gz') or args.fastqs[0].endswith('.fastq') or \
args.fastqs[0].endswith('.fq'): # it's fastq
args.fastqs = [[f] for f in args.fastqs] # make it a matrix
else: # it's TSV
args.fastqs = read_tsv(args.fastqs[0])
for i, fastqs in enumerate(args.fastqs):
if args.paired_end and len(fastqs) != 2:
raise argparse.ArgumentTypeError(
'Need 2 fastqs per replicate for paired end.')
if not args.paired_end and len(fastqs) != 1:
raise argparse.ArgumentTypeError(
'Need 1 fastq per replicate for single end.')
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def parse_arguments(debug=False):
parser = argparse.ArgumentParser(prog='ENCODE DCC adapter trimmer.',
description='')
parser.add_argument('fastqs',
nargs='+',
type=str,
help='TSV file path or list of FASTQs. \
FASTQs must be compressed with gzip (with .gz). \
Use TSV for multiple fastqs to be merged later. \
row=merge_id, col=end_id).')
parser.add_argument('--auto-detect-adapter',
action='store_true',
help='Automatically detect/trim adapters \
(supported system: Illumina, Nextera and smallRNA).')
parser.add_argument(
'--cutadapt-param',
type=str,
default='-e 0.1 -m 5',
help='Parameters for cutadapt '
'(default: -e 0.1 -m 5; err_rate=0.1, min_trim_len=5).')
parser.add_argument(
'--adapter',
type=str,
help='One adapter to use for all fastqs. '
'This will override individual adapters defined in --adapters.')
parser.add_argument('--adapters',
nargs='+',
type=str,
help='TSV file path or list of adapter strings. '
'Use TSV for multiple fastqs to be merged later. '
'row=merge_id, col=end_id).')
parser.add_argument('--paired-end',
action="store_true",
help='Paired-end FASTQs.')
parser.add_argument('--nth',
type=int,
default=1,
help='Number of threads to parallelize.')
parser.add_argument('--out-dir',
default='',
type=str,
help='Output directory.')
parser.add_argument('--log-level',
default='INFO',
choices=[
'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'CRITICAL',
'ERROR', 'CRITICAL'
],
help='Log level')
args = parser.parse_args()
# parse fastqs command line
if args.fastqs[0].endswith('.gz') or args.fastqs[0].endswith('.fastq') or \
args.fastqs[0].endswith('.fq'): # it's fastq
args.fastqs = [[f] for f in args.fastqs] # make it a matrix
else: # it's TSV
args.fastqs = read_tsv(args.fastqs[0])
# parse --adapters command line
if args.adapters:
if os.path.exists(args.adapters[0]): # it's TSV
args.adapters = read_tsv(args.adapters[0])
else:
args.adapters = [[a] for a in args.adapters] # make it a matrix
# if adapter not given
if args.adapter or not args.adapters: # fill empty string in adapter list
args.adapters = copy.deepcopy(args.fastqs)
for i, adapters in enumerate(args.adapters):
for j, adapter in enumerate(adapters):
args.adapters[i][j] = args.adapter if args.adapter else ''
# check if fastqs, adapers have same/correct dimension
if len(args.adapters) != len(args.fastqs):
raise argparse.ArgumentTypeError(
'fastqs and adapters dimension mismatch.')
for i, fastqs in enumerate(args.fastqs):
if args.paired_end and len(fastqs) != 2:
raise argparse.ArgumentTypeError(
'Need 2 fastqs per replicate for paired end.')
if not args.paired_end and len(fastqs) != 1:
raise argparse.ArgumentTypeError(
'Need 1 fastq per replicate for single end.')
if len(fastqs) != len(args.adapters[i]):
raise argparse.ArgumentTypeError(
'fastqs and adapters dimension mismatch.')
log.setLevel(args.log_level)
log.info(sys.argv)
return args