def test_translate(self):
'''Test translate works in each frame'''
tmp = 'tmp.translated.fa'
for i in range(3):
tasks.translate(os.path.join(data_dir, 'sequences_test_translate.fa'), tmp, frame=i)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_translate.fa.frame' + str(i)), tmp))
os.unlink(tmp)
def test_translate(self):
'''Test translate works in each frame'''
tmp = 'tmp.translated.fa'
for i in range(3):
tasks.translate(os.path.join(data_dir, 'sequences_test_translate.fa'), tmp, frame=i)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_translate.fa.frame' + str(i)), tmp))
os.unlink(tmp)
def run(description):
parser = argparse.ArgumentParser(
description = 'Translates all sequences in input file. Output is always FASTA format',
usage = 'fastaq translate [options] <infile> <outfile>')
parser.add_argument('--frame', type=int, choices=[0,1,2], help='Frame to translate [%(default)s]', default=0)
parser.add_argument('infile', help='Name of file to be translated')
parser.add_argument('outfile', help='Name of output FASTA file')
options = parser.parse_args()
tasks.translate(options.infile, options.outfile, frame=options.frame)
def run(description):
parser = argparse.ArgumentParser(
description="Translates all sequences in input file. Output is always FASTA format",
usage="fastaq translate [options] <infile> <outfile>",
)
parser.add_argument("--frame", type=int, choices=[0, 1, 2], help="Frame to translate [%(default)s]", default=0)
parser.add_argument("infile", help="Name of file to be translated")
parser.add_argument("outfile", help="Name of output FASTA file")
options = parser.parse_args()
tasks.translate(options.infile, options.outfile, frame=options.frame)
