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)