def create_reader(options, parser, counter_magnitude="M"):
interleaved = bool(options.interleaved_input)
input1 = options.interleaved_input if interleaved else options.input1
input2 = qualfile = None
if options.paired and not interleaved:
input2 = options.input2
else:
qualfile = options.input2
try:
reader = open_reader(input1, file2=input2, qualfile=qualfile,
colorspace=options.colorspace, fileformat=options.format,
interleaved=interleaved, single_input_read=options.single_input_read)
except (UnknownFileType, IOError) as e:
parser.error(e)
qualities = reader.delivers_qualities
# Wrap reader in subsampler
if options.subsample:
reader = subsample(reader, options.subsample)
# Wrap reader in batch iterator
batch_size = options.batch_size or 1000
reader = BatchIterator(reader, batch_size, options.max_reads)
# Wrap iterator in progress bar
if options.progress:
from .progress import create_progress_reader
reader = create_progress_reader(
reader, options.progress, batch_size, options.max_reads,
counter_magnitude)
return (reader, (input1, input2), qualities, qualfile is not None)
def create_reader(options, parser, counter_magnitude="M"):
interleaved = bool(options.interleaved_input)
input1 = options.interleaved_input if interleaved else options.input1
input2 = qualfile = None
if options.paired and not interleaved:
input2 = options.input2
else:
qualfile = options.input2
try:
reader = open_reader(input1, file2=input2, qualfile=qualfile,
colorspace=options.colorspace, fileformat=options.format,
interleaved=interleaved, single_input_read=options.single_input_read)
except (UnknownFileType, IOError) as e:
parser.error(e)
qualities = reader.delivers_qualities
# Wrap reader in subsampler
if options.subsample:
reader = subsample(reader, options.subsample)
# Wrap reader in batch iterator
batch_size = options.batch_size or 1000
reader = BatchIterator(reader, batch_size, options.max_reads)
# Wrap iterator in progress bar
if options.progress:
from .progress import create_progress_reader
reader = create_progress_reader(
reader, options.progress, batch_size, options.max_reads,
counter_magnitude)
return (reader, (input1, input2), qualities, qualfile is not None)
def main():
parser = ArgumentParser()
parser.add_argument("-a", "--aligner", choices=('adapter', 'insert'))
parser.add_argument("-m", "--mode", choices=('time','run'), default='run')
parser.add_argument("-o", "--outfile")
parser.add_argument("-1", "--fastq1", default='test1.fq')
parser.add_argument("-2", "--fastq2", default='test2.fq')
parser.add_argument("-i", "--iters", default=10)
args = parser.parse_args()
aligner = create_adapter() if args.aligner == 'adapter' else create_insert()
if args.mode == 'time':
t = 0
for i in range(args.iters):
reader = open_reader(args.fastq1, args.fastq2)
t += time_process(reader, aligner)
reader.close()
print("Average time: {}".format(t / args.iters))
else:
run_process(reader, aligner)
def main():
parser = ArgumentParser()
parser.add_argument("-a", "--aligner", choices=('adapter', 'insert'))
parser.add_argument("-m", "--mode", choices=('time', 'run'), default='run')
parser.add_argument("-o", "--outfile")
parser.add_argument("-1", "--fastq1", default='test1.fq')
parser.add_argument("-2", "--fastq2", default='test2.fq')
parser.add_argument("-i", "--iters", default=10)
args = parser.parse_args()
aligner = create_adapter() if args.aligner == 'adapter' else create_insert(
)
if args.mode == 'time':
t = 0
for i in range(args.iters):
reader = open_reader(args.fastq1, args.fastq2)
t += time_process(reader, aligner)
reader.close()
print("Average time: {}".format(t / args.iters))
else:
run_process(reader, aligner)