def test_run(self):
with tempfile.NamedTemporaryFile(prefix="anoise") as fp:
args = ["clean", "CAGGGAGCTGGAAAGATTYGC", fp.name, "--input", self.raw_path]
try:
dispatch.main(args)
self.assertLinesEqual(self.fa_path, fp.name + ".fa")
finally:
for f in glob.iglob(fp.name + ".*"):
os.remove(f)
def test_run(self):
with tempfile.NamedTemporaryFile(prefix='anoise') as fp:
args = [
'clean', 'CAGGGAGCTGGAAAGATTYGC', fp.name, '--input',
self.raw_path
]
try:
dispatch.main(args)
self.assertLinesEqual(self.fa_path, fp.name + '.fa')
finally:
for f in glob.iglob(fp.name + '.*'):
os.remove(f)
def test_run_pyronoise(self):
sff_path = os.path.abspath(self.sff_path)
sff_name = os.path.basename(sff_path)
args = ['pyronoise', sff_name, '--mpi-args', '-np 2', '--stub', 'test']
with tempdir(prefix='pyronoise-') as td:
with cd(td):
self.assertEqual(td, os.getcwd())
shutil.copy(sff_path, sff_name)
dispatch.main(args)
self.assertEqual(td, os.getcwd())
try:
self.assertLinesEqual(self.expected_path, 'test-pnoise_cd.fa')
self.assertLinesEqual(self.mapping_path, 'test-pnoise.mapping')
finally:
for f in ('test-pnoise_cd.fa', 'test-pnoise.mapping'):
if os.path.exists(f):
os.remove(f)
#!/usr/bin/env python
if __name__ == '__main__':
from anoisetools.scripts.dispatch import main
main()
