def test_changing_working_dir(self):
"""Clustalw BaseCommand should change according to WorkingDir"""
c = Clustalw(WorkingDir='/tmp/clustaltest')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/clustaltest','/"; ','clustalw -align']))
c = Clustalw(WorkingDir='/tmp/clustaltest/')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/clustaltest/','/"; ','clustalw -align']))
c = Clustalw()
c.WorkingDir = '/tmp/clustaltest2/'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/clustaltest2/','/"; ','clustalw -align']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/clustaltest')
rmdir('/tmp/clustaltest2')
def test_tree_outputtree(self):
"""Clustalw tree should work correctly with outputtree"""
c = Clustalw(params={'-tree':None,'-outputtree':'dist',\
'-infile':'/tmp/ct/align1'},WorkingDir='/tmp/ct/')
c.Parameters['-align'].off()
res = c()
self.assertEqual(res['Tree'].name, '/tmp/ct/align1.ph')
self.assertEqual(res['TreeInfo'].name, '/tmp/ct/align1.dst')
res.cleanUp()
def test_stdout_input_as_string(self):
"""Clustalw input_as_string shoud function as expected"""
c = Clustalw(WorkingDir='/tmp/ct')
res = c('/tmp/ct/seq1.txt')
self.assertEqual(cw_vers.sub("", res['StdOut'].read()),
cw_vers.sub("", self.stdout1))
self.assertEqual(res['StdErr'].read(), '')
self.assertEqual(cw_vers.sub("", res['Align'].read()),
cw_vers.sub("", self.aln1))
self.assertEqual(res['Dendro'].read(), self.dnd1)
res.cleanUp()
def test_profile_newtree(self):
"""Clustalw profile should work correctly with new/usetree"""
c = Clustalw(params={'-profile':None,'-profile1':'/tmp/ct/seq1.txt',\
'-profile2':'/tmp/ct/seq2.txt','-newtree1':'lala'},\
WorkingDir='/tmp/ct')
c.Parameters['-align'].off()
res = c()
self.assertEqual(res['Align'], None)
self.assertEqual(res['Dendro1'].name, '/tmp/ct/lala')
self.assertEqual(res['Dendro2'].name, '/tmp/ct/seq2.dnd')
res.cleanUp()
def test_sequences_newtree(self):
"""Clustalw sequences should work correctly with new/usetree"""
c = Clustalw(params={'-sequences':None,'-newtree':'lala',\
'-profile1':'/tmp/ct/align1','-profile2':'/tmp/ct/seq2.txt'},\
WorkingDir='/tmp/ct')
c.Parameters['-align'].off()
res = c()
self.assertEqual(res['Align'], None)
self.assertEqual(res['Dendro'].name, '/tmp/ct/lala')
res.cleanUp()
#is this a bug in clustal. It's creating an empty file 'seq2.aln'
#but doesn't report it in the stdout
remove('/tmp/ct/seq2.aln')
def test_base_command(self):
"""Clustalw BaseCommand should return the correct BaseCommand"""
c = Clustalw()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','clustalw -align']))
c.Parameters['-infile'].on('seq.txt')
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ',\
'clustalw -infile="seq.txt" -align']))
c.Parameters['-align'].off()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','clustalw -infile="seq.txt"']))
c.Parameters['-nopgap'].on()
c.Parameters['-infile'].off()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','clustalw -nopgap']))
def test_changing_working_dir(self):
"""Clustalw BaseCommand should change according to WorkingDir"""
c = Clustalw(WorkingDir='/tmp/clustaltest')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/clustaltest','/"; ','clustalw -align']))
c = Clustalw(WorkingDir='/tmp/clustaltest/')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/clustaltest/','/"; ','clustalw -align']))
c = Clustalw()
c.WorkingDir = '/tmp/clustaltest2/'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/clustaltest2/','/"; ','clustalw -align']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/clustaltest')
rmdir('/tmp/clustaltest2')
def test_stdout_input_as_multiline_string(self):
"""Clustalw input_as_multiline_string should function as expected"""
c = Clustalw(InputHandler='_input_as_multiline_string',\
WorkingDir='/tmp/ct')
res = c(self.multiline1)
name = c.Parameters['-infile'].Value
out = self.stdout1.split('\n')
out[16] =\
'Guide tree file created: ['+name.rsplit(".")[0]+'.dnd]'
out[23] =\
'CLUSTAL-Alignment file created ['+name.rsplit(".")[0]+'.aln]'
self.assertEqual(cw_vers.sub("", res['StdOut'].read()),
cw_vers.sub("", '\n'.join(out)))
self.assertEqual(res['StdErr'].read(), '')
self.assertEqual(cw_vers.sub("", res['Align'].read()),
cw_vers.sub("", self.aln1))
self.assertEqual(res['Dendro'].read(), self.dnd1)
res.cleanUp()
def test_alignment_trees(self):
"""Clustalw alignment should work correctly with new/usetree"""
c = Clustalw(params={'-quicktree':True,'-type':'DNA','-gapopen':10},\
WorkingDir='/tmp/ct')
res = c('/tmp/ct/seq1.txt')
self.assertEqual(res['Align'].name, '/tmp/ct/seq1.aln')
self.assertEqual(res['Dendro'].name, '/tmp/ct/seq1.dnd')
res.cleanUp()
c.Parameters['-usetree'].on('/tmp/ct/tree1')
c.Parameters['-output'].on('PHYLIP')
res = c('/tmp/ct/seq1.txt')
self.assertEqual(res['Align'].name, '/tmp/ct/seq1.phy')
self.assertEqual(res['Dendro'].name, '/tmp/ct/tree1')
res.cleanUp()
c.Parameters['-newtree'].on('newtree')
c.Parameters['-outfile'].on('outfile')
res = c('/tmp/ct/seq1.txt')
self.assertEqual(res['Align'].name, c.WorkingDir + 'outfile')
self.assertEqual(res['Dendro'].name, c.WorkingDir + 'newtree')
res.cleanUp()
def test_stdout_input_as_lines_local(self):
"""Clustalw input_as_lines should function as expected"""
c = Clustalw(InputHandler='_input_as_lines',
WorkingDir=self.temp_dir_space)
res = c(self.lines1)
#get info on input file name and change output accordingly
name = c.Parameters['-infile'].Value
out = self.stdout1.split('\n')
out[16] =\
'Guide tree file created: ['+name.rsplit(".")[0]+'.dnd]'
out[23] =\
'CLUSTAL-Alignment file created ['+name.rsplit(".")[0]+'.aln]'
self.assertEqual(cw_vers.sub("", res['StdOut'].read()),
cw_vers.sub("", '\n'.join(out)))
self.assertEqual(res['StdErr'].read(), '')
self.assertEqual(cw_vers.sub("", res['Align'].read()),
cw_vers.sub("", self.aln1))
self.assertEqual(res['Dendro'].read(), self.dnd1)
res.cleanUp()
