def align_to_refenence(self, noalign, minp = 0.9):
refaln = self.refjson.get_alignment(fout = self.tmp_refaln)
fprofile = self.refjson.get_hmm_profile(self.hmmprofile)
# if there is no hmmer profile in json file, build it from scratch
if not fprofile:
hmm = hmmer(self.cfg, refaln)
fprofile = hmm.build_hmm_profile()
hm = hmmer(config = self.cfg, refalign = refaln , query = self.tmpquery, refprofile = fprofile, discard = noalign, seqs = self.seqs, minp = minp)
self.epa_alignment = hm.align()
def align_to_refenence(self, noalign, minp=0.9):
refaln = self.refjson.get_alignment(fout=self.tmp_refaln)
fprofile = self.refjson.get_hmm_profile(self.hmmprofile)
# if there is no hmmer profile in json file, build it from scratch
if not fprofile:
hmm = hmmer(self.cfg, refaln)
fprofile = hmm.build_hmm_profile()
hm = hmmer(config=self.cfg,
refalign=refaln,
query=self.tmpquery,
refprofile=fprofile,
discard=noalign,
seqs=self.seqs,
minp=minp)
self.epa_alignment = hm.align()
def build_hmm_profile(self, json_builder):
print "Building the HMMER profile...\n"
# this stupid workaround is needed because RAxML outputs the reduced
# alignment in relaxed PHYLIP format, which is not supported by HMMER
refalign_fasta = self.cfg.tmp_fname("%NAME%_ref_reduced.fa")
self.reduced_refalign_seqs.write(outfile=refalign_fasta)
hmm = hmmer(self.cfg, refalign_fasta)
fprofile = hmm.build_hmm_profile()
json_builder.set_hmm_profile(fprofile)
def build_hmm_profile(self, json_builder):
print "Building the HMMER profile...\n"
# this stupid workaround is needed because RAxML outputs the reduced
# alignment in relaxed PHYLIP format, which is not supported by HMMER
refalign_fasta = self.cfg.tmp_fname("%NAME%_ref_reduced.fa")
self.reduced_refalign_seqs.write(outfile=refalign_fasta)
hmm = hmmer(self.cfg, refalign_fasta)
fprofile = hmm.build_hmm_profile()
json_builder.set_hmm_profile(fprofile)
