def testOSTSequenceWDir(self):
# OST sequence as input, with working dir should work
query_seq = seq.CreateSequence('1AKE.B',
'MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRA'+
'AVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQ'+
'EDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDV'+
'PDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDV'+
'TGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYYYS'+
'KEAEAGNTKYAKVDGTKPVAEVRADLEKILG')
tmpdir = tempfile.mkdtemp()
self.hh = hhblits.HHblits(query_seq, self.hhroot, working_dir=tmpdir)
self.assertEqual(self.hh.filename, os.path.join(tmpdir,
'query_hhblits.fasta'))
self.assertEqual(self.hh.working_dir, tmpdir)
self.hh.needs_cleanup = True
def testA3mToCSFileExists(self):
# test A3mToCS to work with a given hhmake_file name
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
csfile = self.hh.A3MToCS("testfiles/testali.a3m",
cs_file='testfiles/test.seq219',
options={'-alphabet' :
os.path.join(self.hh.hhlib_dir,
'data',
'cs219.lib')})
self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219'))
def testA3mToProfileWithoutFileName(self):
# test A3mToProfile to work without a given hhmake_file name
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
hhfile = self.hh.A3MToProfile("testfiles/testali.a3m")
with open(hhfile) as tfh:
tlst = tfh.readlines()
with open("testfiles/test.hmm") as efh:
elst = efh.readlines()
self.assertEqual(len(elst), len(tlst))
for i in range(0, len(elst)):
if not elst[i].startswith(('FILE', 'COM', 'DATE')):
self.assertEqual(elst[i], tlst[i])
os.remove(hhfile)
def testSearchWorking(self):
# successful search
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
search_file = self.hh.Search("testfiles/testali.a3m",
'testfiles/hhblitsdb/hhblitsdb')
with open(search_file) as tfh:
tlst = tfh.readlines()
with open("testfiles/test.hhr") as efh:
elst = efh.readlines()
self.assertEqual(len(elst), len(tlst))
for i in range(0, len(elst)):
if not elst[i].startswith(('Date', 'Command')):
self.assertEqual(elst[i], tlst[i])
def testFileNoWDir(self):
# we have a sequence but no working dir
self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot)
self.assertEqual(self.hh.filename[-10:], 'seq2.fasta')
def testFileNoExists(self):
# test on calling with a non-existing fasta file
with self.assertRaises(IOError) as ioe:
hhblits.HHblits('notthere.fasta', self.hhroot)
self.assertEqual(ioe.exception.errno, 2)
self.assertEqual(ioe.exception.strerror, 'No such file or directory')