def __init__(self, seq, seqdb, verbose=False, **kwargs):
"""
seq: the sequence to search with
a single or a list of SeqRecords
seqdb: the sequence database to search
a single or a list of SeqRecords
keyword arguments: other arguments to jackhmmer - see HMMER docs
"""
#Can only have one query
if not isinstance(seq, SeqRecord):
raise ValueError("seq must be a SeqRecord, not \'{}\'".format(type(seq)))
if not is_protein(seq):
raise ValueError("seq be have a ProteinAlphabet, not \'{}\'".format(a))
if isinstance(seqdb, SeqRecord):
seqdb = [seqdb,]
self.args = self.getArgs(**kwargs)
self.matches = []
self.hmms = []
#apply unique ids to the targets
self.seq = wrap_seqrecords([seq,])
self.seqdb=wrap_seqrecords(seqdb)
targets = []
for t in self.seqdb:
if is_protein(t):
targets.append(t)
elif is_dna(t):
targets += list(tools.getSixFrameTranslation(t))
else:
raise ValueError(
"Targets must have a DNAAlphabet or a ProteinAlphabet, not \'{}\'"
.format(t.seq.alphabet))
self._do_search(self.seq, targets, self.args)
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))
