def test_ebov_refine2(self):
inDir = util.file.get_test_input_path(self)
inFasta = os.path.join(inDir, 'expected.ebov.refine1.fasta')
refine1Fasta = util.file.mkstempfname('.refine1.fasta')
refine2Fasta = util.file.mkstempfname('.refine2.fasta')
shutil.copy(inFasta, refine1Fasta)
tools.picard.CreateSequenceDictionaryTool().execute(refine1Fasta, overwrite=True)
tools.novoalign.NovoalignTool().index_fasta(refine1Fasta)
assembly.refine_assembly(
refine1Fasta,
os.path.join(util.file.get_test_input_path(), 'G5012.3.mini.bam'),
refine2Fasta,
# normally -r Random, but for unit tests, we want deterministic behavior
novo_params='-r None -l 40 -x 20 -t 100',
min_coverage=3)
actual = str(Bio.SeqIO.read(refine2Fasta, 'fasta').seq)
expected = str(Bio.SeqIO.read(os.path.join(inDir, 'expected.ebov.refine2.fasta'), 'fasta').seq)
self.assertEqual(actual, expected)
def test_ebov_refine2(self):
inDir = util.file.get_test_input_path(self)
inFasta = os.path.join(inDir, 'expected.ebov.refine1.fasta')
refine1Fasta = util.file.mkstempfname('.refine1.fasta')
refine2Fasta = util.file.mkstempfname('.refine2.fasta')
shutil.copy(inFasta, refine1Fasta)
tools.picard.CreateSequenceDictionaryTool().execute(refine1Fasta,
overwrite=True)
tools.novoalign.NovoalignTool().index_fasta(refine1Fasta)
assembly.refine_assembly(
refine1Fasta,
os.path.join(util.file.get_test_input_path(), 'G5012.3.mini.bam'),
refine2Fasta,
# normally -r Random, but for unit tests, we want deterministic behavior
novo_params='-r None -l 40 -x 20 -t 100',
min_coverage=3)
actual = str(Bio.SeqIO.read(refine2Fasta, 'fasta').seq)
expected = str(
Bio.SeqIO.read(os.path.join(inDir, 'expected.ebov.refine2.fasta'),
'fasta').seq)
self.assertEqual(actual, expected)