def test_changing_working_dir(self): """RNAfold: BaseCommand should be ok after changing the working dir""" #changing in initialization temp_dir = tempfile.mkdtemp() r = RNAfold(WorkingDir=temp_dir) self.assertEqual(r.BaseCommand,\ 'cd "%s/"; RNAfold -d1 -T 37 -S 1.07'%(temp_dir)) #changing afterwards r = RNAfold() r.WorkingDir = temp_dir self.assertEqual(r.BaseCommand,\ 'cd "%s/"; RNAfold -d1 -T 37 -S 1.07'%(temp_dir)) rmdir(temp_dir)
def test_changing_working_dir(self): """RNAfold: BaseCommand should be ok after changing the working dir""" #changing in initialization temp_dir = tempfile.mkdtemp() r = RNAfold(WorkingDir=temp_dir) self.assertEqual(r.BaseCommand,\ 'cd "%s/"; RNAfold -d1 -T 37 -S 1.07'%(temp_dir)) #changing afterwards r = RNAfold() r.WorkingDir = temp_dir self.assertEqual(r.BaseCommand,\ 'cd "%s/"; RNAfold -d1 -T 37 -S 1.07'%(temp_dir)) rmdir(temp_dir)
def test_base_command(self): """RNAfold: BaseCommand should be ok for different parameter settings""" r = RNAfold() working_dir = getcwd() obs = r.BaseCommand.split() exp = [ 'cd', '"%s/";' % getcwd(), 'RNAfold', '-d1', '-T', '37', '-S', '1.07' ] self.assertEqualItems(obs, exp) r.Parameters['-noLP'].on() obs = r.BaseCommand.split() exp = ['cd','"%s/";' % getcwd(),'RNAfold','-d1','-noLP','-T','37',\ '-S','1.07'] self.assertEqualItems(obs, exp) r.Parameters['Temp'].on(15) obs = r.BaseCommand.split() exp = ['cd','"%s/";' % getcwd(),'RNAfold','-d1','-noLP','-T','15', \ '-S','1.07'] self.assertEqualItems(obs, exp) r.Parameters['-d'].off() obs = r.BaseCommand.split() exp = [ 'cd', '"%s/";' % getcwd(), 'RNAfold', '-noLP', '-T', '15', '-S', '1.07' ] self.assertEqualItems(obs, exp)
def predict_ss(self, method="RNAfold"): """it creats /tmp/ss.fa and runs various methods for ss prediction""" # make tmp file f = open('/tmp/ss.fa', 'w') f.write('>test\n') f.write(self.seq) f.close() # run prediction if method == "RNAsubopt": r = RNAsubopt(WorkingDir="/tmp") res = r([self.seq]) return str(res['StdOut'].read()).strip() if method == "ipknot": self.ss_log = commands.getoutput('ipknot /tmp/ss.fa') return '\n'.join(self.ss_log.split('\n')[2:]) if method == "contextfold": cmd = "cd /home/magnus/work/opt/ContextFold_1_00 && java -cp bin contextFold.app.Predict in:" + self.seq self.ss_log = commands.getoutput(cmd) return '\n'.join(self.ss_log.split('\n')[1:]) if method == "centroid_fold": self.ss_log = commands.getoutput('centroid_fold /tmp/ss.fa') return '\n'.join(self.ss_log.split('\n')[2:]) if method == 'RNAfold': r = RNAfold(WorkingDir="/tmp") res = r([self.seq]) self.ss_log = res['StdOut'].read() return self.ss_log.strip().split('\n')[-1].split()[0]
def test_get_result_paths_mixed_seq(self): """RNAfold: _get_result_paths() should work on partly named seq""" r = RNAfold() res = r(self.mixed_seq) self.assertEqualItems(res.keys(),\ ['StdOut','StdErr','ExitStatus','SS','DP','namedseq1_ss',\ 'namedseq1_dp']) res.cleanUp()
def test_stdout(self): """RNAfold: StdOut should be as expected""" r = RNAfold() exp = '\n'.join(['>namedseq1','AUAGCUAGCUAUGCGCUAGC',\ '...((((((.....)))))) ( -8.30)','ACGGCUAUAGCUAGCGA',\ '...((((....)))).. ( -3.20)','GCUAGCUAUUAUAUAUA',\ '................. ( 0.00)'])+'\n' res = r(self.mixed_seq) obs = res['StdOut'].read() self.assertEqual(obs, exp) res.cleanUp()
def test_get_result_paths_unnamed_seq(self): """RNAfold: _get_result_paths() should work on unnamed seq""" r = RNAfold() res = r(self.unnamed_seq) self.assertEqualItems(res.keys(),\ ['StdOut','StdErr','ExitStatus','SS','DP']) self.failUnless(res['DP'] is None) self.failUnless(res['SS'] is not None) self.failUnless(res['StdOut'] is not None) self.failUnless(res['StdErr'] is None) self.assertEqual(res['ExitStatus'], 0) res.cleanUp()
def test_get_result_paths_working_dir(self): """RNAfold: _get_result_paths() should work with diff working dir""" r = RNAfold(WorkingDir=self.temp_dir) res = r(self.unnamed_seq) self.assertEqualItems(res.keys(),\ ['StdOut','StdErr','ExitStatus','SS','DP']) self.failUnless(res['DP'] is None) self.failUnless(res['SS'] is not None) self.failUnless(isinstance(res['SS'], file)) self.failUnless(res['StdOut'] is not None) self.failUnless(res['StdErr'] is None) self.assertEqual(res['ExitStatus'], 0) res.cleanUp()
def test_get_result_paths_parameter(self): """RNAfold: _get_result_paths() should work with diff parameters""" r = RNAfold() r.Parameters['-p'].on() res = r(self.unnamed_seq) self.assertEqualItems(list(res.keys()),\ ['StdOut','StdErr','ExitStatus','SS','DP']) self.assertTrue(res['DP'] is not None) self.assertTrue(res['SS'] is not None) self.assertTrue(res['StdOut'] is not None) self.assertTrue(res['StdErr'] is None) self.assertEqual(res['ExitStatus'],0) res.cleanUp()
def test_stdout_input_as_path(self): """RNAfold: StdOut with input_as_path""" r = RNAfold(InputHandler='_input_as_path') f = open('/tmp/rnatestfile', 'w') f.write('\n'.join(self.mixed_seq2)) f.close() exp = '\n'.join(['>namedseq2','AUAGCUAGCUAUGCGCUAGC',\ '...((((((.....)))))) ( -8.30)','ACGGCUAUAGCUAGCGA',\ '...((((....)))).. ( -3.20)','GCUAGCUAUUAUAUAUA',\ '................. ( 0.00)'])+'\n' res = r('/tmp/rnatestfile') obs = res['StdOut'].read() self.assertEqual(obs, exp) res.cleanUp() remove('/tmp/rnatestfile')