class SimpleBlastRunTestCase(unittest.TestCase):
def setUp(self):
self.my_blast_db = "/Users/kdrew/astral/1.75/astral95.1.75"
self.my_blast_file = "./createdbs/data/test_seq.fasta"
self.my_blast_outfile = "./createdbs/data/test_seq.blast.xml"
#self.my_blast_exe = "/usr/bin/blastall"
self.my_blast_exe = "/Users/patrick/.local/share/blast-2.2.18/bin/blastall"
self.e_value_threshold = 1e-8
self.length_threshold = .85
self.processors = 3
#kdrew: compare to command line
#blastall -p "blastp" -d /home/kdrew/astral/1.75/astral95.1.75 -i /home/kdrew/scripts/function_prediction_python/createdbs/data/test_seq.fasta -m 7 -e 1e-8
self.ba = AstralBlastFilter(self.my_blast_exe, self.my_blast_db, self.my_blast_file, self.e_value_threshold, self.length_threshold, blast_processors=self.processors)
self.records = self.ba.runBlast()
self.filtered = self.ba.filterBlast(self.records)
self.ba.writeFasta(self.filtered)
def testNumFiltered(self):
assert 5 == len(self.filtered), 'too many records returned'
def testKeyFiltered(self):
assert '3' in self.filtered, 'wrong record filtered'
assert '1' not in self.filtered, 'wrong record filtered'
def testSuperfamily(self):
assert 'a.51.1' == self.filtered[str(1605014)].superfamily, 'wrong superfamily'
def testFastaOut(self):
assert 1515 == os.path.getsize(self.my_blast_file.rpartition('.')[0]+"_filtered.fasta"), 'wrong file size'
class SimpleCDHitRunTestCase(unittest.TestCase):
def setUp(self):
print "in cdhit test setup"
self.my_blast_db = "/Users/kdrew/astral/1.75/astral95.1.75"
self.my_blast_file = "./createdbs/data/test_seq_cdHit.fasta"
self.my_blast_outfile = "./createdbs/data/test_seq_cdHit.blast.xml"
#self.my_blast_exe = "/usr/bin/blastall"
self.my_blast_exe = "/Users/patrick/.local/share/blast-2.2.18/bin/blastall"
self.e_value_threshold = 1e-8
self.length_threshold = .85
self.processors = 3
self.my_fasta_file = "./createdbs/data/test_seq_cdHit_filtered.fasta"
self.my_cd_hit_exe = "/Users/kdrew/programs/cd-hit/cd-hit"
self.identity_cutoff = .95
self.length_cutoff = .5
sql_user="******"
sql_password="******"
sql_host="localhost"
#kdrew: compare to command line
#blastall -p "blastp" -d /home/kdrew/astral/1.75/astral95.1.75 -i /home/kdrew/scripts/function_prediction_python/createdbs/data/test_seq.fasta -m 7 -e 1e-8
self.ba = AstralBlastFilter(self.my_blast_exe, self.my_blast_db, self.my_blast_file, self.e_value_threshold, self.length_threshold, blast_processors=self.processors)
self.records = self.ba.runBlast()
print "after blast"
self.filtered = self.ba.filterBlast(self.records)
print "after filter"
self.ba.writeFasta(self.filtered)
self.mg = Mygo(sql_user,sql_password, sql_host, e_codes =['TAS','IDA','IMP'], db_name="mygo")
self.mg.connect()
print "conneted to mygo"
self.mgIEA = Mygo(sql_user,sql_password, sql_host, e_codes =['IEA'], db_name="mygo")
self.mgIEA.connect()
#kdrew: compare to command line
#~/cd-hit/cd-hit/cd-hit -i test_seq_filtered.fasta -o test_seq_filtered.cd_hit.out -c .95 -s .5
self.cd = CDHitGO(self.my_cd_hit_exe, self.my_fasta_file, id_c=self.identity_cutoff, len_c=self.length_cutoff)
self.cd.runCDHit()
self.cd.printCDHit()
def testFastaOut(self):
assert 1395 == os.path.getsize(self.my_fasta_file.rpartition('.')[0]+".cd_hit.out"), 'wrong file size'
#kdrew: function deprecated
#def testGetGoTerms(self):
#clstr_terms = self.cd.getClusterGoTerms(self.mg)
#assert 0 == len(clstr_terms['196690']), 'incorrect number of terms returned'
#assert 21 == len(clstr_terms['1605014']), 'incorrect number of terms returned'
# clstr_terms = self.cd.getClusterGoTerms(self.mgIEA)
# assert 33 == len(clstr_terms['196690']), 'incorrect number of terms returned'
# assert 0 == len(clstr_terms['1605014']), 'incorrect number of terms returned'
def testGetClusters(self):
clstr_terms = self.cd.getClusters(self.filtered, self.mg, mustHaveGO=False)
assert 1 == len(clstr_terms['196690']), 'incorrect number of terms returned'
assert 22 == len(clstr_terms['1605014']), 'incorrect number of terms returned'
try:
x = clstr_terms['3']
assert False, 'sequence was not removed'
except KeyError:
assert True
clstr_terms = self.cd.getClusters(self.filtered, self.mgIEA, mustHaveGO=False)
assert 34 == len(clstr_terms['196690']), 'incorrect number of terms returned'
assert 1 == len(clstr_terms['1605014']), 'incorrect number of terms returned'
