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'):
TestExamples.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),
f'--hintsfile={datadir}/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, outputfolder=htmldir)
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, outputfolder=htmldir)
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, outputfolder=htmldir)
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, outputfolder=htmldir)
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',
f'--extrinsicCfgFile={configdir}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, outputfolder=htmldir)
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, outputfolder=htmldir)
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, outputfolder=htmldir)
