def test_invalid_taxid(self):
with scratch_file() as out:
with open(out, 'w') as h:
class _Args(object):
database_file = config.ncbi_master_db
taxids = 'horace,hilda'
taxnames = None
seq_info = None
verbosity = 0
out_file = h
self.assertEqual(taxtable.action(_Args()), 1)
def test_taxids(self):
with scratch_file() as out:
with open(out, 'w') as h:
class _Args(object):
database_file = config.ncbi_master_db
taxids = config.data_path('taxids1.txt')
taxnames = None
seq_info = None
verbosity = 0
out_file = h
self.assertEqual(taxtable.action(_Args()), 0)
self.assertEqual(refpkg.md5file(out), '88ed5643d4754c60d5c472ff0b298f0f')
def test_seqinfo(self):
with tempfile.TemporaryFile() as tf, \
open(config.data_path('simple_seqinfo.csv')) as ifp:
class _Args(object):
database_file = config.ncbi_master_db
taxids = None
taxnames = None
seq_info = ifp
out_file = tf
verbosity = 0
self.assertEqual(taxtable.action(_Args()), 0)
# No output check at present
self.assertTrue(tf.tell() > 0)
def test_invalid_taxid(self):
with scratch_file() as out:
with open(out, 'w') as h:
class _Args(object):
database_file = config.ncbi_master_db
taxids = 'horace,hilda'
taxnames = None
seq_info = None
verbosity = 0
out_file = h
full = False
self.assertNotEqual(taxtable.action(_Args()), 0)
def test_seqinfo(self):
with tempfile.TemporaryFile() as tf, \
open(config.data_path('simple_seqinfo.csv')) as ifp:
class _Args(object):
database_file = config.ncbi_master_db
taxids = None
taxnames = None
seq_info = ifp
out_file = tf
verbosity = 0
full = False
self.assertEqual(taxtable.action(_Args()), 0)
# No output check at present
self.assertTrue(tf.tell() > 0)
def test_seqinfo(self):
with tempfile.TemporaryFile() as tf, \
open(config.data_path('simple_seqinfo.csv')) as ifp:
class _Args(object):
url = 'sqlite:///' + config.ncbi_master_db
schema = None
valid = False
ranked = False
tax_ids = None
taxnames = None
seq_info = ifp
out = tf
verbosity = 0
clade_ids = None
taxtable = None
self.assertIsNone(taxtable.action(_Args()))
# No output check at present
self.assertTrue(tf.tell() > 0)