def testReversedIntegration(self):
# Reverse-complement the genome, insert stages in the reverse direction
# and check that the product is still the same
spec = dict.copy(self.spec)
genome = SeqIO.read(spec['genome']['filename'], 'genbank')
# Won't work on Windows - it won't allow the open file to be opened again
rev_genome_file = tempfile.NamedTemporaryFile(delete=True)
SeqIO.write(genome.reverse_complement(), rev_genome_file, 'genbank')
rev_genome_file.flush()
spec['genome']['filename'] = rev_genome_file.name
# Calculate target location in reversed genome. Input locations are
# 1-indexed, so need to add 1 to find equivalent reverse location.
old_start_loc = spec['genome']['start']
spec['genome']['start'] = len(genome) - spec['genome']['end'] + 1
spec['genome']['end'] = len(genome) - old_start_loc + 1
spec['genome']['strand'] = -spec['genome']['strand']
assembly = InchwormAssembly.from_spec(spec)
# Check that genome is reversed correctly
self.assertEqual(str(assembly.genome.reverse_complement().seq.upper()),
str(self.assembly.genome.seq.upper()))
# Check that the predicted product is correct
for stage_num in range(5+1):
self.assertEqual(' '.join(str(assembly.product(stage_num).reverse_complement().seq.upper())),
' '.join(str(self.assembly.product(stage_num).seq.upper())))
# Check that the generated product matches the predicted product
# Equivalent to TestInchwormAssembly.testRunStages()
run_stages_output = assembly.run_stages()
for stage in range(1, 5+1):
run_stages_product = run_stages_output[stage-1]['genome'].seq.upper()
expected_product = assembly.product(stage).seq.upper()
self.assertEqual(str(run_stages_product), str(expected_product))
def setUp(self):
os.chdir(os.path.dirname(os.path.realpath(__file__)))
self.spec = yaml.load(open('vioABEDC_input.yaml'))
self.assembly = InchwormAssembly.from_spec(self.spec)
