def influenza_impute(self, aligner):
outImputeFasta = util.file.mkstempfname('.fasta')
expected = os.path.join(self.inDir, 'expected.influenza.impute.'+aligner+'.fasta')
# ensure we can run impute_from_reference from the output of order_and_orient
# without errors, but don't actually check the output
assembly.impute_from_reference(
self.outOrientFasta,
self.refFasta,
outImputeFasta,
minLengthFraction=0.8,
minUnambig=0.2,
replaceLength=5,
newName='test_influenza.genome',
aligner=aligner)
def influenza_impute(self, aligner):
outImputeFasta = util.file.mkstempfname('.fasta')
expected = os.path.join(
self.inDir, 'expected.influenza.impute.' + aligner + '.fasta')
# ensure we can run impute_from_reference from the output of order_and_orient
# without errors, but don't actually check the output
assembly.impute_from_reference(self.outOrientFasta,
self.refFasta,
outImputeFasta,
minLengthFraction=0.8,
minUnambig=0.2,
replaceLength=5,
newName='test_influenza.genome',
aligner=aligner)
def test_small_mummer(self):
inDir = util.file.get_test_input_path(self)
outFasta = util.file.mkstempfname('.fasta')
expected = os.path.join(inDir, 'expected.sub.ebov.impute.fasta')
assembly.impute_from_reference(
os.path.join(inDir, 'test.pseudo.fasta'),
os.path.join(inDir, 'ref.sub.ebov.fasta'),
outFasta,
minLengthFraction=0.8,
minUnambig=0.2,
replaceLength=5,
newName='test_sub-EBOV.genome',
aligner='mummer')
self.assertEqual(
str(Bio.SeqIO.read(outFasta, 'fasta').seq),
str(Bio.SeqIO.read(expected, 'fasta').seq))
def test_varicella_big_muscle(self):
inDir = util.file.get_test_input_path(self)
outFasta = util.file.mkstempfname('.fasta')
expected = os.path.join(inDir, 'expected.hhv3.muscle.fasta')
inDirBase = util.file.get_test_input_path()
assembly.impute_from_reference(
os.path.join(inDirBase, 'TestOrderAndOrient', 'expected.hhv3.fasta'),
os.path.join(inDirBase, 'TestOrderAndOrient', 'ref.hhv3.fasta'),
outFasta,
minLengthFraction=0.8,
minUnambig=0.6,
replaceLength=55,
newName='HHV3-test')
self.assertEqual(
str(Bio.SeqIO.read(outFasta, 'fasta').seq),
str(Bio.SeqIO.read(expected, 'fasta').seq))
def test_small_mummer(self):
inDir = util.file.get_test_input_path(self)
outFasta = util.file.mkstempfname('.fasta')
expected = os.path.join(inDir, 'expected.sub.ebov.impute.fasta')
assembly.impute_from_reference(os.path.join(inDir,
'test.pseudo.fasta'),
os.path.join(inDir,
'ref.sub.ebov.fasta'),
outFasta,
minLengthFraction=0.8,
minUnambig=0.2,
replaceLength=5,
newName='test_sub-EBOV.genome',
aligner='mummer')
self.assertEqual(str(Bio.SeqIO.read(outFasta, 'fasta').seq),
str(Bio.SeqIO.read(expected, 'fasta').seq))
def test_varicella_big_muscle(self):
inDir = util.file.get_test_input_path(self)
outFasta = util.file.mkstempfname('.fasta')
expected = os.path.join(inDir, 'expected.hhv3.muscle.fasta')
inDirBase = util.file.get_test_input_path()
assembly.impute_from_reference(
os.path.join(inDirBase, 'TestOrderAndOrient', 'expected.hhv3.fasta'),
os.path.join(inDirBase, 'TestOrderAndOrient', 'ref.hhv3.fasta'),
outFasta,
minLengthFraction=0.8,
minUnambig=0.6,
replaceLength=55,
newName='HHV3-test')
self.assertEqual(
str(Bio.SeqIO.read(outFasta, 'fasta').seq),
str(Bio.SeqIO.read(expected, 'fasta').seq))