def run(description):
parser = argparse.ArgumentParser(
description = 'Deinterleaves sequence file, so that reads are written alternately between two output files',
usage = 'fastaq deinterleave [options] <infile> <out_fwd> <out_rev>')
parser.add_argument('--fasta_out', action='store_true', help='Use this to write output as fasta (default is same as input)', default=False)
parser.add_argument('infile', help='Name of fasta/q file to be deinterleaved')
parser.add_argument('out_fwd', help='Name of output fasta/q file of forwards reads')
parser.add_argument('out_rev', help='Name of output fasta/q file of reverse reads')
options = parser.parse_args()
tasks.deinterleave(options.infile, options.out_fwd, options.out_rev, fasta_out=options.fasta_out)
def test_deinterleave(self):
'''deinterleave should deal with an interleaved file correctly'''
tmp_1 = 'tmp.deinterleaved_1.fa'
tmp_2 = 'tmp.deinterleaved_2.fa'
tasks.deinterleave(os.path.join(data_dir, 'sequences_test_interleaved.fa'), tmp_1, tmp_2)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_1.fa'), tmp_1))
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_2.fa'), tmp_2))
tasks.deinterleave(os.path.join(data_dir, 'sequences_test_interleaved.fq'), tmp_1, tmp_2, fasta_out=True)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_1.fa'), tmp_1))
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_2.fa'), tmp_2))
with self.assertRaises(tasks.Error):
tasks.deinterleave(os.path.join(data_dir, 'sequences_test_interleaved_bad.fa'), tmp_1, tmp_2)
os.unlink(tmp_1)
os.unlink(tmp_2)
def test_deinterleave(self):
'''deinterleave should deal with an interleaved file correctly'''
tmp_1 = 'tmp.deinterleaved_1.fa'
tmp_2 = 'tmp.deinterleaved_2.fa'
tasks.deinterleave(os.path.join(data_dir, 'sequences_test_interleaved.fa'), tmp_1, tmp_2)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_1.fa'), tmp_1))
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_2.fa'), tmp_2))
tasks.deinterleave(os.path.join(data_dir, 'sequences_test_interleaved.fq'), tmp_1, tmp_2, fasta_out=True)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_1.fa'), tmp_1))
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_2.fa'), tmp_2))
with self.assertRaises(tasks.Error):
tasks.deinterleave(os.path.join(data_dir, 'sequences_test_interleaved_bad.fa'), tmp_1, tmp_2)
os.unlink(tmp_1)
os.unlink(tmp_2)
