def run(description):
parser = argparse.ArgumentParser(
description = 'Makes all combinations of sequences in input file by using all possibilities of redundant bases. e.g. ART could be AAT or AGT. Assumes input is nucleotides, not amino acids',
usage = 'fastaq expand_nucleotides <infile> <outfile>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output file')
options = parser.parse_args()
tasks.expand_nucleotides(
options.infile,
options.outfile,
)
def test_expand_nucleoties(self):
'''Test expand_nucleotides'''
tmp = 'tmp.expanded'
fq_in = os.path.join(data_dir, 'tasks_test_expend_nucleotides.in.fq')
fa_in = os.path.join(data_dir, 'tasks_test_expend_nucleotides.in.fa')
fq_expected = os.path.join(data_dir, 'tasks_test_expend_nucleotides.out.fq')
fa_expected = os.path.join(data_dir, 'tasks_test_expend_nucleotides.out.fa')
tasks.expand_nucleotides(fq_in, tmp)
self.assertTrue(filecmp.cmp(fq_expected, tmp, shallow=False))
os.unlink(tmp)
tasks.expand_nucleotides(fa_in, tmp)
self.assertTrue(filecmp.cmp(fa_expected, tmp, shallow=False))
os.unlink(tmp)
def test_expand_nucleoties(self):
'''Test expand_nucleotides'''
tmp = 'tmp.expanded'
fq_in = os.path.join(data_dir, 'tasks_test_expend_nucleotides.in.fq')
fa_in = os.path.join(data_dir, 'tasks_test_expend_nucleotides.in.fa')
fq_expected = os.path.join(data_dir, 'tasks_test_expend_nucleotides.out.fq')
fa_expected = os.path.join(data_dir, 'tasks_test_expend_nucleotides.out.fa')
tasks.expand_nucleotides(fq_in, tmp)
self.assertTrue(filecmp.cmp(fq_expected, tmp, shallow=False))
os.unlink(tmp)
tasks.expand_nucleotides(fa_in, tmp)
self.assertTrue(filecmp.cmp(fa_expected, tmp, shallow=False))
os.unlink(tmp)