def run(description):
parser = argparse.ArgumentParser(
description='Converts CAF file to FASTQ format',
usage='fastaq caf_to_fastq [options] <infile> <outfile>')
parser.add_argument('infile', help='Name of input CAF file.')
parser.add_argument('outfile', help='Name of output FASTQ file')
parser.add_argument(
'-c',
'--clip',
action='store_true',
help=
'Use clipping info to clip reads, if present in the input CAF file (as lines of the form "Clipping QUAL start end"). Default is to not clip'
)
parser.add_argument(
'-l',
'--min_length',
type=int,
help='Minimum length of sequence to output [%(default)s]',
default=1,
metavar='INT')
options = parser.parse_args()
tasks.caf_to_fastq(options.infile,
options.outfile,
trim=options.clip,
min_length=options.min_length)
def test_caf_to_fastq_default(self):
'''Test caf_to_fastq with no filtering'''
tmpfile = 'tmp.fq'
tasks.caf_to_fastq(os.path.join(data_dir, 'caf_test.caf'), tmpfile)
self.assertTrue(
filecmp.cmp(os.path.join(
data_dir, 'caf_test.to_fastq.no_trim.min_length_0.fq'),
tmpfile,
shallow=False))
os.unlink(tmpfile)
def test_caf_to_fastq_trim_and_min_length(self):
'''Test caf_to_fastq with trimming and min_length'''
tmpfile = 'tmp.fq'
tasks.caf_to_fastq(os.path.join(data_dir, 'caf_test.caf'),
tmpfile,
trim=True,
min_length=6)
self.assertTrue(
filecmp.cmp(os.path.join(data_dir,
'caf_test.to_fastq.trim.min_length_6.fq'),
tmpfile,
shallow=False))
os.unlink(tmpfile)
def run(description):
parser = argparse.ArgumentParser(
description="Converts CAF file to FASTQ format", usage="fastaq caf_to_fastq [options] <infile> <outfile>"
)
parser.add_argument("infile", help="Name of input CAF file.")
parser.add_argument("outfile", help="Name of output FASTQ file")
parser.add_argument(
"-c",
"--clip",
action="store_true",
help='Use clipping info to clip reads, if present in the input CAF file (as lines of the form "Clipping QUAL start end"). Default is to not clip',
)
parser.add_argument(
"-l",
"--min_length",
type=int,
help="Minimum length of sequence to output [%(default)s]",
default=1,
metavar="INT",
)
options = parser.parse_args()
tasks.caf_to_fastq(options.infile, options.outfile, trim=options.clip, min_length=options.min_length)
def test_caf_to_fastq_trim_and_min_length(self):
'''Test caf_to_fastq with trimming and min_length'''
tmpfile = 'tmp.fq'
tasks.caf_to_fastq(os.path.join(data_dir, 'caf_test.caf'), tmpfile, trim=True, min_length=6)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'caf_test.to_fastq.trim.min_length_6.fq'), tmpfile, shallow=False))
os.unlink(tmpfile)
def test_caf_to_fastq_default(self):
'''Test caf_to_fastq with no filtering'''
tmpfile = 'tmp.fq'
tasks.caf_to_fastq(os.path.join(data_dir, 'caf_test.caf'), tmpfile)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'caf_test.to_fastq.no_trim.min_length_0.fq'), tmpfile, shallow=False))
os.unlink(tmpfile)
