def testProtHint(self):
os.chdir(testDir + "/test_ProtHint")
subprocess.call("../../bin/prothint.py genome.fasta proteins.fasta --geneMarkGtf genemark.gtf \
--workdir output --cleanup", shell=True)
self.assertEqual(common.compareFiles("output/prothint.gff", "test_output/prothint.gff"), 0)
self.assertEqual(common.compareFiles("output/evidence.gff", "test_output/evidence.gff"), 0)
shutil.rmtree("output")
def testProcessOutput(self):
prothint.workDir = testDir + "/test_processSpalnOutput"
os.chdir(prothint.workDir)
shutil.copyfile("Spaln/spaln.gff", "Spaln/spaln_orig.gff")
prothint.processSpalnOutput("diamond/diamond.out")
shutil.move("Spaln/spaln_orig.gff", "Spaln/spaln.gff")
self.assertEqual(
common.compareFiles("prothint.gff", "test_prothint.gff"), 0)
self.assertEqual(
common.compareFiles("evidence.gff", "test_evidence.gff"), 0)
self.assertEqual(
common.compareFiles("prothint_augustus.gff",
"test_prothint_augustus.gff"), 0)
os.remove("prothint.gff")
os.remove("evidence.gff")
os.remove("prothint_augustus.gff")
def testIterNoSeedChange(self):
# Test case in which the seed genes do not change, only their IDs change
os.chdir(testDir + "/test_iter")
subprocess.call(
"../../bin/prothint.py genome.fasta proteins.fasta --geneSeeds genemarkPrevIDChange.gtf \
--prevGeneSeeds genemarkPrev.gtf --prevSpalnGff prevSpaln.gff --workdir output",
shell=True)
self.assertEqual(
common.compareFiles("output/prothint_augustus.gff",
"test_output/prothint_augustus.gff"), 0)
shutil.rmtree("output")
def testIter(self):
os.chdir(testDir + "/test_iter")
subprocess.call(
"../../bin/prothint.py genome.fasta proteins.fasta --geneSeeds genemark.gtf \
--prevGeneSeeds genemarkPrev.gtf --prevSpalnGff prevSpaln.gff --workdir output",
shell=True)
self.assertEqual(
common.compareFiles("output/prothint.gff",
"test_output/prothint.gff"), 0)
self.assertEqual(
common.compareFiles("output/evidence.gff",
"test_output/evidence.gff"), 0)
self.assertEqual(
common.compareFiles("output/diamond/diamond.out",
"test_output/diamond/diamond.out"), 0)
self.assertEqual(
common.compareFiles("output/uniqueSeeds.gtf",
"test_output/uniqueSeeds.gtf"), 0)
self.assertEqual(
common.compareFiles("output/prevHints.gff",
"test_output/prevHints.gff"), 0)
shutil.rmtree("output")