def test_parse_blast(self):
""" Parse a blast result with multiple entries """
fn = os.path.join(self.datadir, "2061976712.xml")
results = BLASTUtilities.parse_blast(fn,25)
self.assertEqual(len(results.titles),25)
self.assertEqual(len(results.evalues),25)
self.assertEqual(len(results.scores),25)
self.assertEqual(len(results.bits),25)
def test_parse_blast(self):
""" Parse a blast result with multiple entries """
fn = os.path.join(self.datadir, "2061976712.xml")
results = BLASTUtilities.parse_blast(fn, 25)
self.assertEqual(len(results.titles), 25)
self.assertEqual(len(results.evalues), 25)
self.assertEqual(len(results.scores), 25)
self.assertEqual(len(results.bits), 25)
def test_do_blast(self):
""" Test that a BLAST subprocess runs """
fn_sequence = os.path.join(self.datadir, "2061973757.fasta")
fn_database = os.path.join(self.datadir, "mini_nr", "proteins")
parser = SeqIO.parse(fn_sequence, "fasta")
S = parser.next()
identifier = "nothing"
fn_output= BLASTUtilities.do_blast(S.seq.tostring(),identifier, fn_database)
self.assertTrue(os.path.exists(fn_output),"BLAST did not produce the output file")
results = BLASTUtilities.parse_blast(fn_output)
self.assertEqual(len(results.titles),1)
self.assertAlmostEqual(947.577, results.bits[0],delta=0.001, msg="Score not correct")
self.assertAlmostEqual(0, results.evalues[0],delta=1e-5, msg="E-value not correct")
os.remove(fn_output)
def test_do_blast(self):
""" Test that a BLAST subprocess runs """
fn_sequence = os.path.join(self.datadir, "2061973757.fasta")
fn_database = os.path.join(self.datadir, "mini_nr", "proteins")
parser = SeqIO.parse(fn_sequence, "fasta")
S = parser.next()
identifier = "nothing"
fn_output = BLASTUtilities.do_blast(S.seq.tostring(), identifier,
fn_database)
self.assertTrue(os.path.exists(fn_output),
"BLAST did not produce the output file")
results = BLASTUtilities.parse_blast(fn_output)
self.assertEqual(len(results.titles), 1)
self.assertAlmostEqual(947.577,
results.bits[0],
delta=0.001,
msg="Score not correct")
self.assertAlmostEqual(0,
results.evalues[0],
delta=1e-5,
msg="E-value not correct")
os.remove(fn_output)
