def test_changing_working_dir(self):
"""RNAsubopt: BaseCommand should be ok after changing the working dir
"""
temp_dir = tempfile.mkdtemp()
#changing in initialization
r = RNAsubopt(WorkingDir=temp_dir)
self.assertEqual(r.BaseCommand,\
'cd "%s/"; RNAsubopt -e 1 -d2 -T 37'%(temp_dir))
#changing afterwards
r = RNAsubopt()
r.WorkingDir = temp_dir
self.assertEqual(r.BaseCommand,\
'cd "%s/"; RNAsubopt -e 1 -d2 -T 37'%(temp_dir))
rmdir(temp_dir)
def test_changing_working_dir(self):
"""RNAsubopt: BaseCommand should be ok after changing the working dir
"""
temp_dir = tempfile.mkdtemp()
#changing in initialization
r = RNAsubopt(WorkingDir=temp_dir)
self.assertEqual(r.BaseCommand,\
'cd "%s/"; RNAsubopt -e 1 -d2 -T 37'%(temp_dir))
#changing afterwards
r = RNAsubopt()
r.WorkingDir = temp_dir
self.assertEqual(r.BaseCommand,\
'cd "%s/"; RNAsubopt -e 1 -d2 -T 37'%(temp_dir))
rmdir(temp_dir)
def test_base_command(self):
"""RNAsubopt: BaseCommand should be ok for different parameter settings
"""
r = RNAsubopt()
obs = r.BaseCommand.split()
exp = [
'cd',
'"%s/";' % getcwd(), 'RNAsubopt', '-e', '1', '-d2', '-T', '37'
]
self.assertEqualItems(obs, exp)
r.Parameters['-nsp'].on('GA')
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAsubopt','-e','1','-d2','-nsp','GA',\
'-T','37']
self.assertEqualItems(obs, exp)
r.Parameters['Temp'].on(15)
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAsubopt','-e','1','-d2','-nsp','GA',\
'-T','15']
self.assertEqualItems(obs, exp)
r.Parameters['-d'].off()
obs = r.BaseCommand.split()
exp = ['cd','"%s/";' % getcwd(),'RNAsubopt','-e','1','-nsp','GA','-T',\
'15']
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(self):
"""RNAsubopt: _get_result_paths() should create the right dict entries
"""
r = RNAsubopt()
seq = ['AUAGCUAGCUAUGCGCUAGCGGAUUAGCUAGCUAGCGA',\
'ucgaucgaucagcuagcuauuauauaua']
res = r(seq)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus'])
self.failUnless(res['StdOut'] is not None)
self.failUnless(res['StdErr'] is None)
self.assertEqual(res['ExitStatus'], 0)
res.cleanUp()
r = RNAsubopt({'-s':None,'-lodos':None,'-d':3,'-logML':None,\
'-noLP':None,'-4':None,'-noGU':None,'-noCloseGU':None})
res = r(seq)
self.assertEqualItems(res.keys(),\
['StdOut','StdErr','ExitStatus'])
self.failUnless(res['StdOut'] is not None)
self.failUnless(res['StdErr'] is None)
#self.assertEqual(res['ExitStatus'],0) #platform-dependent?
res.cleanUp()
def test_stdout_input_as_path_space(self):
"""RNAsubopt: StdOut with input_as_path and space in filename"""
mixed_seq2 = [
'>namedseq2', 'AUAGCUAGCUAUGCGCUAGC', 'ACGGCUAUAGCUAGCGA',
'gcuagcuauuauauaua'
]
r = RNAsubopt(InputHandler='_input_as_path')
f = open('/tmp/rna test file', 'w')
f.write('\n'.join(mixed_seq2))
f.close()
exp = '\n'.join([
'> namedseq2 [100]', 'AUAGCUAGCUAUGCGCUAGC -830 100',
'...((((((.....)))))) -8.30', 'ACGGCUAUAGCUAGCGA -320 100',
'...(((......))).. -2.30', '...((((....)))).. -3.20',
'GCUAGCUAUUAUAUAUA 0 100', '................. 0.00'
]) + '\n'
res = r('/tmp/rna test file')
obs = res['StdOut'].read()
self.assertEqual(obs, exp)
res.cleanUp()
remove('/tmp/rna test file')
def test_stdout(self):
"""RNAsubopt: StdOut should be as expected"""
r = RNAsubopt()
seq = ['AUAGCUAGCUAUGCGCUAGCGGAUUAGCUAGCUAGCGA',\
'ucgaucgaucagcuagcuauuauauaua']
exp = '\n'.join(
['AUAGCUAGCUAUGCGCUAGCGGAUUAGCUAGCUAGCGA -1720 100',
'.(((((((((.(((....)))....))))))))).... -16.20',
'.(((((((((((.((....)).)).))))))))).... -17.20',
'.((((((((((..((....))...)))))))))).... -16.60',
'.((((((((((.((....))....)))))))))).... -16.40',
'.(((((((((((((....)))...)))))))))).... -16.90',
'.(((((((((((.((....)).).)))))))))).... -17.20',
'UCGAUCGAUCAGCUAGCUAUUAUAUAUA 0 100',
'......(((.((....)))))....... 0.70',
'..........((....)).......... 0.60',
'..((....)).................. 0.90',
'............................ 0.00']) + '\n'
res = r(seq)
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
res.cleanUp()