def setUp(self):
lysozyme = ("MKALIVLGLVLLSVTVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGY"
"NTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVAC"
"AKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV")
self.lyz = oma.OrthologFinder(lysozyme)
stragg = ('YYYYYYYYYYYVVVVVVVVVVVVBBBBBBBBBBBAAAAAAAAAAANNNNNNNNNNN'
'MMMMMMMMMMMWWWWWWWWWWWWWCCCCCCCCCCSSSSSSSSSS')
self.aggregate = oma.OrthologFinder(stragg)
def test_empty_input_HOG(self):
"""Checks that the correct exception is raised when an empty sequence is entered"""
fs = oma.OrthologFinder("")
with self.assertRaises(oma.SequenceError) as cm:
fs.get_HOGs()
err = cm.exception
self.assertEqual(str(err), 'Input sequence is empty!')
def setUpClass(cls):
cls.filepath = tools.testRoot() + "consScore"
with open((cls.filepath + os.sep + 'CDC48Aseq.txt'), 'r') as file:
arabidopsisCDC48A = file.read()
cls.CDC48A = oma.OrthologFinder(arabidopsisCDC48A)
with open((cls.filepath + os.sep + 'OMA_get_id.txt'), 'r') as file:
OMA_id_response = file.read()
cls.response = bytes(OMA_id_response, 'utf-8')
with open((cls.filepath + os.sep + 'orhtolog_response.txt'),
'r') as file:
ortho_response = file.read()
cls.oresponse = bytes(ortho_response, 'utf-8')
with open((cls.filepath + os.sep + 'fasta_response.txt'), 'r') as file:
fasta_response = file.read()
cls.fresponse = bytes(fasta_response, 'utf-8')
with open((cls.filepath + os.sep + 'ATN1_HOGS.txt'), 'r') as file:
HOG_response = file.read()
cls.hresponse = bytes(HOG_response, 'utf-8')
with open((cls.filepath + os.sep + 'hog_content.txt'), 'r') as file:
level_response = file.read()
cls.lvlresponse = bytes(level_response, 'utf-8')
def call_orthologs(self):
"""
Retrieves the HOGS of the input sequence. This is done by querying the OMA online database.
"""
if os.path.isfile(self.input):
with open(self.input, "r") as file:
sequence = file.read()
ortholog_call = oma.OrthologFinder(sequence)
else:
ortholog_call = oma.OrthologFinder(self.input)
try:
self.orthologs = ortholog_call.get_HOGs()
except RequestException:
self.orthologs = ortholog_call.get_orthologs()
with open("%s.orth" % (self.name), "w") as o_file:
o_file.write(self.orthologs)
return os.getcwd() + os.sep + "%s.orth" % (self.name)
def call_orthologs(self):
"""
Retrieves the HOG or the orthologs of the entered sequence by querying the OMA database
"""
ortholog_call = oma.OrthologFinder(self.sequence)
try:
self.orthologs = ortholog_call.get_HOGs()
except exceptions.RequestException:
self.orthologs = ortholog_call.get_orthologs()
with open("%s.orth" % (self.name), 'w') as o_file:
o_file.write(self.orthologs)
return os.getcwd() + os.sep + '%s.orth' % (self.name)