def prepare(self):
"""
If the target is a PDBModel its sequence will be written
to disc as a fasta file.
If it is already fasta file the path to the file will be passed on.
"""
try:
## if target is a PDBModel or simple sequence string
if isinstance(self.target, PDBModel):
fastaSeq, self.fastaID = MT.fasta(self.target)
## write fasta sequence file
seq = open(self.f_in, 'w')
seq.write(fastaSeq)
seq.close()
elif self.__verify_fasta(self.target):
if type(self.target) is list:
seq = open(self.f_in, 'w')
seq.writelines(self.target)
seq.close()
else:
## else assume it is a fasta sequence file
self.f_in = self.target
else:
raise HmmerError, 'cannot interpret target %r' % self.target
except OSError, why:
msg = 'Cannot write temporary fasta file %s' % self.f_in
msg += '\nError: %r' % why
raise HmmerError, msg
def prepare( self ):
"""
If the target is a PDBModel its sequence will be written
to disc as a fasta file.
If it is already fasta file the path to the file will be passed on.
"""
try:
## if target is a PDBModel or simple sequence string
if isinstance(self.target, PDBModel):
fastaSeq, self.fastaID = MT.fasta( self.target )
## write fasta sequence file
seq = open( self.f_in, 'w' )
seq.write( fastaSeq )
seq.close()
elif self.__verify_fasta(self.target):
if type(self.target) is list:
seq = open( self.f_in, 'w' )
seq.writelines( self.target )
seq.close()
else:
## else assume it is a fasta sequence file
self.f_in = self.target
else:
raise HmmerError, 'cannot interpret target %r' % self.target
except OSError, why:
msg = 'Cannot write temporary fasta file %s' % self.f_in
msg += '\nError: %r' % why
raise HmmerError, msg
def prepare( self ):
"""
If the target id a PDBModel its sequence will be written
to disc as a fasta file.
If it is a fasta file the path to the file will be passed on.
"""
## if target is a PDBModel
if isinstance( self.target, PDBModel):
fastaSeq, self.fastaID = MT.fasta( self.target )
## write fasta sequence file
seq = open( self.fName, 'w' )
seq.write( fastaSeq )
seq.close()
## else assume it is a fasta sequence file
else:
if self.__verify_fasta(self.target):
self.fName = self.target
def align(self, model, hits):
"""
Performs alignment
If there is more than one hit with the profile, the sequence will
be subdevided and the alignment will be performed on each part.
a final merger profile for the profile will be returned.
@param model: structure model
@type model: PDBModel
@param hits: list with matching sections from L{searchHmmdb}
@type hits: [[int,int]]
@return: fastaSeq hmmSeq repete hmmGap::
fastaSeq - sequence
hmmSeq - matching positions in profile
repete - number of repetes of the profile
hmmGap - list with gaps (deletions in search sequence) for
each repete
@rtype: str, str, int, [int]
"""
try:
fastaSeq, self.fastaID = MT.fasta(model)
fastaSeq = fastaSeq.split()[1]
l = len(fastaSeq)
## sub sequence alignment
j = 0
repete = 0
hmmGap = []
for h in hits:
start = h[0] - 1
stop = h[1]
sub_fastaSeq, self.fastaID = MT.fasta(model, start, stop)
## write sub-fasta sequence file
fName = self.sub_fastaFile
sub_seq = open(fName, 'w')
sub_seq.write(sub_fastaSeq)
sub_seq.close()
## get sub-alignmnet
align = HmmerAlign(self.hmmFile,
self.sub_fastaFile,
self.fastaID,
verbose=self.verbose,
log=self.log)
sub_fastaSeq, sub_hmmSeq = align.run()
## remove positions corresponding to insertions in
## search sequence
sub_fastaSeq, sub_hmmSeq, del_hmm = \
self.removeGapInSeq( sub_fastaSeq, sub_hmmSeq )
hmmGap += [del_hmm]
## rebuild full lenght hmmSeq from sub_hmmSeq
sub_hmmSeq = '.' * start + sub_hmmSeq + '.' * (l - stop)
if j == 0:
hmmSeq = sub_hmmSeq
if j != 0:
hmmSeq = self.mergeHmmSeq(hmmSeq, sub_hmmSeq)
j += 1
repete += 1
return fastaSeq, hmmSeq, repete, hmmGap
except IOError, e:
raise HmmerError, "Error creating temporary file %r. "%e.filename+\
"Check that Biskit.settings.temDirShared is accessible!\n"+\
"See also .biskit/settings.cfg!"
def align( self, model, hits ):
"""
Performs alignment
If there is more than one hit with the profile, the sequence will
be subdevided and the alignment will be performed on each part.
a final merger profile for the profile will be returned.
@param model: structure model
@type model: PDBModel
@param hits: list with matching sections from L{searchHmmdb}
@type hits: [[int,int]]
@return: fastaSeq hmmSeq repete hmmGap::
fastaSeq - sequence
hmmSeq - matching positions in profile
repete - number of repetes of the profile
hmmGap - list with gaps (deletions in search sequence) for
each repete
@rtype: str, str, int, [int]
"""
try:
fastaSeq, self.fastaID = MT.fasta( model )
fastaSeq = fastaSeq.split()[1]
l = len(fastaSeq)
## sub sequence alignment
j = 0
repete = 0
hmmGap = []
for h in hits:
start = h[0]-1
stop = h[1]
sub_fastaSeq, self.fastaID = MT.fasta( model, start, stop )
## write sub-fasta sequence file
fName = self.sub_fastaFile
sub_seq = open( fName, 'w' )
sub_seq.write( sub_fastaSeq )
sub_seq.close()
## get sub-alignmnet
align = HmmerAlign( self.hmmFile, self.sub_fastaFile,
self.fastaID, verbose=self.verbose,
log=self.log)
sub_fastaSeq, sub_hmmSeq = align.run()
## remove positions corresponding to insertions in
## search sequence
sub_fastaSeq, sub_hmmSeq, del_hmm = \
self.removeGapInSeq( sub_fastaSeq, sub_hmmSeq )
hmmGap += [ del_hmm ]
## rebuild full lenght hmmSeq from sub_hmmSeq
sub_hmmSeq = '.'*start + sub_hmmSeq + '.'*(l-stop)
if j == 0:
hmmSeq = sub_hmmSeq
if j != 0:
hmmSeq = self.mergeHmmSeq( hmmSeq, sub_hmmSeq )
j+= 1
repete += 1
return fastaSeq, hmmSeq, repete, hmmGap
except IOError, e:
raise HmmerError, "Error creating temporary file %r. "%e.filename+\
"Check that Biskit.settings.temDirShared is accessible!\n"+\
"See also .biskit/settings.cfg!"