def test_cmalign_from_alignment(self):
"""cmalign_from_alignment should work as expected.
"""
#Align with cmalign_from_alignment without original alignment.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA,include_aln=False)
#Check correct alignment
self.assertEqual(aln.todict(),self.seqs1_aligned)
#Check correct struct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_aligned_struct_string)
#should work with gapped seqs. Need to test this is taken care of
# since cmalign segfaults when there are gaps in the seqs to be aligned.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
#should work with ungapped seqs.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
#should return standard out
aln, struct,stdout = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA,\
return_stdout=True)
#Test that standard out is same length as expected
self.assertEqual(len(stdout.split('\n')),\
len(CMALIGN_STDOUT.split('\n')))
def __call__(self, seq_path, result_path=None, log_path=None, \
failure_path=None, cmbuild_params=None, cmalign_params=None):
log_params = []
# load candidate sequences
candidate_sequences = dict(MinimalFastaParser(open(seq_path,'U')))
# load template sequences
try:
info, template_alignment, struct = list(MinimalRfamParser(open(\
self.Params['template_filepath'],'U'),\
seq_constructor=ChangedSequence))[0]
except RecordError:
raise ValueError, "Template alignment must be in Stockholm format with corresponding secondary structure annotation when using InfernalAligner."
moltype = self.Params['moltype']
#Need to make separate mapping for unaligned sequences
unaligned = SequenceCollection(candidate_sequences,MolType=moltype)
int_map, int_keys = unaligned.getIntMap(prefix='unaligned_')
int_map = SequenceCollection(int_map,MolType=moltype)
#Turn on --gapthresh option in cmbuild to force alignment to full model
if cmbuild_params is None:
cmbuild_params = {}
cmbuild_params.update({'--gapthresh':1.0})
#record cmbuild parameters
log_params.append('cmbuild parameters:')
log_params.append(str(cmbuild_params))
#Turn on --sub option in Infernal, since we know the unaligned sequences
# are fragments.
#Also turn on --gapthresh to use same gapthresh as was used to build
# model
if cmalign_params is None:
cmalign_params = {}
cmalign_params.update({'--sub':True,'--gapthresh':1.0})
#record cmalign parameters
log_params.append('cmalign parameters:')
log_params.append(str(cmalign_params))
#Align sequences to alignment including alignment gaps.
aligned, struct_string = cmalign_from_alignment(aln=template_alignment,\
structure_string=struct,\
seqs=int_map,\
moltype=moltype,\
include_aln=True,\
params=cmalign_params,\
cmbuild_params=cmbuild_params)
#Pull out original sequences from full alignment.
infernal_aligned={}
aligned_dict = aligned.NamedSeqs
for key in int_map.Names:
infernal_aligned[int_keys.get(key,key)]=aligned_dict[key]
#Create an Alignment object from alignment dict
infernal_aligned = Alignment(infernal_aligned,MolType=moltype)
if log_path is not None:
log_file = open(log_path,'w')
log_file.write('\n'.join(log_params))
log_file.close()
if result_path is not None:
result_file = open(result_path,'w')
result_file.write(infernal_aligned.toFasta())
result_file.close()
return None
else:
try:
return infernal_aligned
except ValueError:
return {}
