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')