def test_iterative_prediction(self):
os.chdir(default_wd)
reffolder = self.get_ref_folder()
resfolder = self.get_res_folder()
os.mkdir(resfolder)
species_list = ['nasonia', 'zebrafish', 'tomato']
# run augustus several times with different parameter sets
for species in species_list:
testtmpfile = os.path.join(
resfolder, 'aug.' + species + '.1-1M_tmp.gff')
self.process([
augustusbin, '--species=' + species,
f'{tmpdir}chr2L.sm.fa', '--softmasking=on',
'--predictionEnd=1000000'
], testtmpfile)
# filter output
testfile = os.path.join(resfolder, 'aug.' + species + '.1-1M.gff')
afilter.pred(testtmpfile, testfile)
os.remove(testtmpfile)
# compare results
self.assertEqualFolders(reffolder, resfolder)
def test_iterative_prediction_with_hints(self):
os.chdir(default_wd)
reffolder = self.get_ref_folder()
resfolder = self.get_res_folder()
os.mkdir(resfolder)
if not os.path.isfile('data/tmp/chr2L.sm.fa'):
TestAugustus.init_test_data()
for i in range(0, 3):
testtmpfile = os.path.join(
resfolder, f'aug.nasonia.hints.{str(i)}_tmp.gff')
self.process([
augustusbin, '--species=nasonia',
f'{tmpdir}chr2L.sm.fa', '--softmasking=on',
'--predictionStart=' + str(i * 2000000),
'--predictionEnd=' + str((i + 1) * 2000000 + 50000),
'--hintsfile=../../docs/tutorial2015/results/hints.gff',
'--extrinsicCfgFile=extrinsic.M.RM.E.W.cfg'
], testtmpfile)
# filter output
testfile = os.path.join(
resfolder, f'aug.nasonia.hints.{str(i)}.gff')
afilter.pred(testtmpfile, testfile)
os.remove(testtmpfile)
# compare results
self.assertEqualFolders(reffolder, resfolder)
def test_alternatives_from_sampling(self):
os.chdir(default_wd)
resfolder = resultdir + self.test_alternatives_from_sampling.__name__ + '/'
os.mkdir(resfolder)
with open(resfolder + 'augustus_tmp.gff', 'w') as file:
cmd = [
augustusbin, '../../examples/autoAug/genome.fa',
'--species=caenorhabditis', '--alternatives-from-sampling=on',
'--minexonintronprob=0.08', '--minmeanexonintronprob=0.4',
'--maxtracks=3'
]
p = subprocess.Popen(cmd,
stdout=file,
stderr=subprocess.PIPE,
universal_newlines=True)
p.wait()
error = p.stderr.read()
p.stderr.close()
self.assertEqual(error, '', error)
# filter output file
self.assertTrue(os.path.isfile(resfolder + 'augustus_tmp.gff'),
'Output file was not created as expected!')
afilter.pred(resfolder + 'augustus_tmp.gff',
resfolder + 'augustus.gff')
os.remove(resfolder + 'augustus_tmp.gff')
# compare results
if TestAugustus.opt_compare:
diff = comp.compare_folder(
refdir + self.test_alternatives_from_sampling.__name__ + '/',
resfolder,
html=TestAugustus.opt_html)
self.assertEqual(diff, '', diff)
def test_format_and_error_out(self):
os.chdir(default_wd)
resfolder = resultdir + self.test_format_and_error_out.__name__ + '/'
os.mkdir(resfolder)
cmd = [
augustusbin, '../../examples/autoAug/genome.fa',
'--species=caenorhabditis', '--gff3=on', '--softmasking=1',
'--outfile=' + resfolder + 'augustus_tmp.gff3',
'--errfile=' + resfolder + 'augustus.err'
]
p = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True)
p.wait()
error = p.stderr.read()
p.stdout.close()
p.stderr.close()
self.assertEqual(error, '', error)
# filter output file
self.assertTrue(os.path.isfile(resfolder + 'augustus_tmp.gff3'),
'Output file was not created as expected!')
afilter.pred(resfolder + 'augustus_tmp.gff3',
resfolder + 'augustus.gff3')
os.remove(resfolder + 'augustus_tmp.gff3')
# compare results
if TestAugustus.opt_compare:
diff = comp.compare_folder(
refdir + self.test_format_and_error_out.__name__ + '/',
resfolder,
html=TestAugustus.opt_html)
self.assertEqual(diff, '', diff)
def test_utr_on(self):
os.chdir(default_wd)
resfolder = resultdir + self.test_utr_on.__name__ + '/'
os.mkdir(resfolder)
with open(resfolder + 'aug_utr_on_tmp.gff', 'w') as file:
p = subprocess.Popen([
augustusbin, '--species=human', '--UTR=on', '--softmasking=0',
'../../examples/example.fa'
],
stdout=file,
stderr=subprocess.PIPE,
universal_newlines=True)
rc = p.wait()
error = p.stderr.read()
p.stderr.close()
self.assertEqual(error, '', error)
self.assertEqual(rc, 0, 'Returncode not 0!')
self.assertTrue(os.path.isfile((resfolder + 'aug_utr_on_tmp.gff')),
'Output file was not created as expected!')
# filter output file
afilter.pred(resfolder + 'aug_utr_on_tmp.gff',
resfolder + 'aug_utr_on.gff')
os.remove(resfolder + 'aug_utr_on_tmp.gff')
# compare results
if TestAugustus.opt_compare:
diff = comp.compare_folder(refdir + self.test_utr_on.__name__ +
'/',
resfolder,
html=TestAugustus.opt_html)
self.assertEqual(diff, '', diff)
def test_iterative_prediction_with_hints(self):
os.chdir(default_wd)
resfolder = resultdir + self.test_iterative_prediction_with_hints.__name__ + '/'
proc_list = []
if not os.path.isfile('data/tmp/chr2L.sm.fa'):
init_test_data()
os.mkdir(resfolder)
for i in range(0, 3):
with open(resfolder + 'aug.nasonia.hints.' + str(i) + '_tmp.gff',
'w') as file:
proc_list.append(
subprocess.Popen([
augustusbin, '--species=nasonia',
'data/tmp/chr2L.sm.fa', '--softmasking=on',
'--predictionStart=' + str(i * 2000000),
'--predictionEnd=' + str((i + 1) * 2000000 + 50000),
'--hintsfile=../docs/tutorial2015/results/hints.gff',
'--extrinsicCfgFile=extrinsic.M.RM.E.W.cfg'
],
stdout=file,
stderr=subprocess.PIPE,
universal_newlines=True))
for p in proc_list:
p.wait()
for p in proc_list:
error = p.stderr.read()
p.stderr.close()
self.assertEqual(error, '', error)
# filter output
for i in range(0, 3):
source = resfolder + 'aug.nasonia.hints.' + str(i) + '_tmp.gff'
self.assertTrue(os.path.isfile(source),
'Output file was not created as expected!')
target = resfolder + 'aug.nasonia.hints.' + str(i) + '.gff'
afilter.pred(source, target)
os.remove(source)
# compare results
if TestAugustus.opt_compare:
diff = comp.compare_folder(
refdir + self.test_iterative_prediction_with_hints.__name__ +
'/',
resfolder,
html=TestAugustus.opt_html)
self.assertEqual(diff, '', diff)
def test_iterative_prediction(self):
os.chdir(default_wd)
resfolder = resultdir + self.test_iterative_prediction.__name__ + '/'
species_list = ['nasonia', 'zebrafish', 'tomato']
proc_list = []
# run augustus several times with different parameter sets
os.mkdir(resfolder)
for species in species_list:
with open(resfolder + 'aug.' + species + '.1-1M_tmp.gff',
'w') as file:
proc_list.append(
subprocess.Popen([
augustusbin, '--species=' + species,
'data/tmp/chr2L.sm.fa', '--softmasking=on',
'--predictionEnd=1000000'
],
stdout=file,
stderr=subprocess.PIPE,
universal_newlines=True))
for p in proc_list:
p.wait()
for p in proc_list:
error = p.stderr.read()
p.stderr.close()
self.assertEqual(error, '', error)
# filter output
for species in species_list:
source = resfolder + 'aug.' + species + '.1-1M_tmp.gff'
self.assertTrue(os.path.isfile(source),
'Output file was not created as expected!')
target = resfolder + 'aug.' + species + '.1-1M.gff'
afilter.pred(source, target)
os.remove(source)
# compare results
if TestAugustus.opt_compare:
diff = comp.compare_folder(
refdir + self.test_iterative_prediction.__name__ + '/',
resfolder,
html=TestAugustus.opt_html)
self.assertEqual(diff, '', diff)
def test_ab_initio_prediction(self):
os.chdir(default_wd)
reffolder = self.get_ref_folder()
resfolder = self.get_res_folder()
testtmpfile = os.path.join(resfolder, 'augustus_tmp.gff')
testfile = os.path.join(resfolder, 'augustus.gff')
os.mkdir(resfolder)
self.process([
augustusbin, f'{exampledir}autoAug/genome.fa', '--softmasking=1',
'--species=caenorhabditis'
], testtmpfile)
# filter output file
afilter.pred(testtmpfile, testfile)
os.remove(testtmpfile)
# compare results
self.assertEqualFolders(reffolder, resfolder)
def test_utr_on(self):
os.chdir(default_wd)
reffolder = self.get_ref_folder()
resfolder = self.get_res_folder()
testtmpfile = os.path.join(resfolder, 'aug_utr_on_tmp.gff')
testfile = os.path.join(resfolder, 'aug_utr_on.gff')
os.mkdir(resfolder)
self.process([
augustusbin, '--species=human', '--UTR=on', '--softmasking=0',
f'{exampledir}example.fa'
], testtmpfile)
# filter output file
afilter.pred(testtmpfile, testfile)
os.remove(testtmpfile)
# compare results
self.assertEqualFolders(reffolder, resfolder)
def test_hints_MPE(self):
reffolder = self.get_ref_folder()
resfolder = self.get_res_folder()
testtmpfile = os.path.join(resfolder, 'aug_hints_MPE_tmp.gff')
testfile = os.path.join(resfolder, 'aug_hints_MPE.gff')
os.chdir(default_wd)
os.mkdir(resfolder)
self.process([
augustusbin, '--species=human', f'--hintsfile={exampledir}hints.gff',
'--extrinsicCfgFile=../../config/extrinsic/extrinsic.MPE.cfg',
f'{exampledir}example.fa'
], testtmpfile)
# filter output file
afilter.pred(testtmpfile, testfile)
os.remove(testtmpfile)
# compare results
self.assertEqualFolders(reffolder, resfolder)
def test_alternatives_from_sampling(self):
os.chdir(default_wd)
reffolder = self.get_ref_folder()
resfolder = self.get_res_folder()
testtmpfile = os.path.join(resfolder, 'augustus_tmp.gff')
testfile = os.path.join(resfolder, 'augustus.gff')
os.mkdir(resfolder)
cmd = [
augustusbin, f'{exampledir}autoAug/genome.fa',
'--species=caenorhabditis', '--alternatives-from-sampling=on',
'--minexonintronprob=0.08', '--minmeanexonintronprob=0.4',
'--maxtracks=3'
]
self.process(cmd, testtmpfile)
# filter output file
afilter.pred(testtmpfile, testfile)
os.remove(testtmpfile)
# compare results
self.assertEqualFolders(reffolder, resfolder)
def test_format_and_error_out(self):
os.chdir(default_wd)
reffolder = self.get_ref_folder()
resfolder = self.get_res_folder()
testtmpfile = os.path.join(resfolder, 'augustus_tmp.gff3')
testfile = os.path.join(resfolder, 'augustus.gff3')
os.mkdir(resfolder)
cmd = [
augustusbin, f'{exampledir}autoAug/genome.fa',
'--species=caenorhabditis', '--gff3=on', '--softmasking=1',
'--outfile=' + testtmpfile,
'--errfile=' + resfolder + '/augustus.err'
]
self.process(cmd)
# filter output file
self.assertTrue(os.path.isfile(testtmpfile),
'Output file was not created as expected!')
afilter.pred(testtmpfile, testfile)
os.remove(testtmpfile)
# compare results
self.assertEqualFolders(reffolder, resfolder)
def test_hints_MPE(self):
dirname = self.test_hints_MPE.__name__
fname = "aug_hints_MPE.gff"
tfname = "aug_hints_MPE_tmp.gff"
os.chdir(default_wd)
resfolder = resultdir + dirname + '/'
os.mkdir(resfolder)
with open(resfolder + tfname, 'w') as file:
p = subprocess.Popen([
augustusbin, '--species=human',
'--hintsfile=../../examples/hints.gff',
'--extrinsicCfgFile=../../config/extrinsic/extrinsic.MPE.cfg',
'../../examples/example.fa'
],
stdout=file,
stderr=subprocess.PIPE,
universal_newlines=True)
rc = p.wait()
error = p.stderr.read()
p.stderr.close()
self.assertEqual(error, '', error)
self.assertEqual(rc, 0, 'Returncode not 0!')
self.assertTrue(os.path.isfile((resfolder + tfname)),
'Output file was not created as expected!')
# filter output file
afilter.pred(resfolder + tfname, resfolder + fname)
os.remove(resfolder + tfname)
# compare results
if TestAugustus.opt_compare:
diff = comp.compare_folder(refdir + dirname + '/',
resfolder,
html=TestAugustus.opt_html)
self.assertEqual(diff, '', diff)
