def _do_search(self, seq, seqdb, args):
seq_file = tempfile.NamedTemporaryFile()
seqdb_file = tempfile.NamedTemporaryFile()
out_file = tempfile.NamedTemporaryFile()
hmm_file = tempfile.NamedTemporaryFile()
SeqIO.write(seq, seq_file, 'fasta')
SeqIO.write(seqdb, seqdb_file, 'fasta')
seq_file.flush()
seqdb_file.flush()
p = Popen(['jackhmmer', '--qformat', 'fasta', '--tformat', 'fasta',
'--chkhmm', hmm_file.name, '--domtblout', out_file.name,] + args +
[seq_file.name, seqdb_file.name,],
stdout=PIPE, stdin=PIPE, stderr=PIPE)
out = p.communicate()
self.matches += matchfile.load(out_file, seq, self.seqdb)
#load the hmms
try:
i = 1
while True:
f = "{}-{}.hmm".format(hmm_file.name, i)
self.hmms.append(hmmfile.read(f)[0])
os.remove(f)
i += 1
except IOError:
pass
out_file.close()
seq_file.close()
seqdb_file.close()
def search(self, hmm, targets, **kwargs):
"""Perform the search
hmm: a file name or an HMM object which has been loaded from a file
targets: the sequences to search - a fasta filename or one or
more Bio.SeqRecord
If the hmm performs searches on Amino Acids and and of the inputs are
DNA sequences, 6-frame translations will be produced automatically
Reverse translations (from Amino Acid to DNA) are not supported
"""
# Load the HMM(s)
if not hasattr(hmm, "__iter__"):
hmm = [hmm,]
#load the file if h is not an HMM object
self.hmm = list()
for h in hmm:
if not isinstance(h, hmmfile.HMM):
self.hmm = self.hmm + hmmfile.read(h)
else:
self.hmm.append(h)
#make sure targets is iterable
if not hasattr(targets, '__iter__') or isinstance(targets, SeqRecord):
targets = [targets,]
self.targets = list(targets)
for t in self.targets:
if not isinstance(t, SeqRecord):
raise ValueError("Search Targets must be SeqRecords")
#apply unique ids
self.targets = wrap_seqrecords(self.targets)
self.hmm = wrap_hmms(self.hmm)
hmm_alpha = self.hmm[0].alph.upper()
for h in self.hmm:
if h.alph.upper() != hmm_alpha:
raise ValueError("The HMMs don't all have the same alphabet")
#get the arguments for HMMER
args = self.getArgs(**kwargs)
#clear the matches
self.matches = []
#Translate targets if necessary
for t in self.targets:
t_alpha = t.alphabet()
if hmm_alpha == 'DNA':
if t_alpha == 'DNA':
self.matches += self._do_search(self.hmm, t, args)
else:
raise ValueError("Cannot search DNA model against non-DNA target")
elif hmm_alpha == 'AMINO':
if t_alpha == 'AMINO':
self.matches += self._do_search(self.hmm, t, args)
elif t_alpha == 'DNA':
#looks like we have to convert
for tt in tools.getSixFrameTranslation(t):
self.matches += self._do_search(self.hmm, tt, args)
else:
raise ValueError("Cannot search Protein model against {} target"
.format(t.seq.alphabet))