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))