def test_capillary_to_pairs(self):
'''Check that capillary reads file converted to paired and unpaired'''
tmp_prefix = 'tmp.cap_to_pairs'
tasks.capillary_to_pairs(
os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa'),
tmp_prefix)
# sequences have been hashed, so could be in any order in
# output files. So need to check contents of files are OK
d_correct_paired = {}
d_correct_unpaired = {}
tasks.file_to_dict(
os.path.join(data_dir,
'sequences_test_cap_to_read_pairs.fa.paired.gz'),
d_correct_paired)
tasks.file_to_dict(
os.path.join(data_dir,
'sequences_test_cap_to_read_pairs.fa.unpaired.gz'),
d_correct_unpaired)
d_test_paired = {}
d_test_unpaired = {}
tasks.file_to_dict(tmp_prefix + '.paired.gz', d_test_paired)
tasks.file_to_dict(tmp_prefix + '.unpaired.gz', d_test_unpaired)
self.assertDictEqual(d_test_paired, d_correct_paired)
self.assertDictEqual(d_test_unpaired, d_correct_unpaired)
os.unlink(tmp_prefix + '.paired.gz')
os.unlink(tmp_prefix + '.unpaired.gz')
def run(description):
parser = argparse.ArgumentParser(
description="Given a file of capillary reads, makes an interleaved file of read pairs (where more than read from same ligation, takes the longest read) and a file of unpaired reads. Replaces the .p1k/.q1k part of read names to denote fwd/rev reads with /1 and /2",
usage="fastaq capillary_to_pairs <infile> <outfiles prefix>",
)
parser.add_argument("infile", help="Name of input fasta/q file")
parser.add_argument("outprefix", help="Prefix of output files", metavar="outfiles prefix")
options = parser.parse_args()
tasks.capillary_to_pairs(options.infile, options.outprefix)
def run(description):
parser = argparse.ArgumentParser(
description=
'Given a file of capillary reads, makes an interleaved file of read pairs (where more than read from same ligation, takes the longest read) and a file of unpaired reads. Replaces the .p1k/.q1k part of read names to denote fwd/rev reads with /1 and /2',
usage='fastaq capillary_to_pairs <infile> <outfiles prefix>')
parser.add_argument('infile', help='Name of input fasta/q file')
parser.add_argument('outprefix',
help='Prefix of output files',
metavar='outfiles prefix')
options = parser.parse_args()
tasks.capillary_to_pairs(options.infile, options.outprefix)
def test_capillary_to_pairs(self):
'''Check that capillary reads file converted to paired and unpaired'''
tmp_prefix = 'tmp.cap_to_pairs'
tasks.capillary_to_pairs(os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa'), tmp_prefix)
# sequences have been hashed, so could be in any order in
# output files. So need to check contents of files are OK
d_correct_paired = {}
d_correct_unpaired = {}
tasks.file_to_dict(os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa.paired.gz'), d_correct_paired)
tasks.file_to_dict(os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa.unpaired.gz'), d_correct_unpaired)
d_test_paired = {}
d_test_unpaired = {}
tasks.file_to_dict(tmp_prefix + '.paired.gz', d_test_paired)
tasks.file_to_dict(tmp_prefix + '.unpaired.gz', d_test_unpaired)
self.assertDictEqual(d_test_paired, d_correct_paired)
self.assertDictEqual(d_test_unpaired, d_correct_unpaired)
os.unlink(tmp_prefix + '.paired.gz')
os.unlink(tmp_prefix + '.unpaired.gz')