def hmmsearch_genome(self,
hmms,
genome,
table='Standard',
decorate=False,
**kwargs):
#translate _genes
with user_message('Translating whole genome in 6 reading frames',
'\n'):
translator = Translator(self._abort_event)
translation = translator.translate_six_frames(genome, table)
if not translation: return None
if isinstance(hmms, str): hmms = [hmms]
results = []
for hmm in hmms:
with user_message('Performing hmm search.'):
hmm_results = self.hmmsearch_recs(hmm, translation, **kwargs)
if not any(len(r) for r in hmm_results): continue
results += hmm_results
#decorate genome
if decorate:
translation = dict((t.id, t) for t in translation)
with user_message('Adding results as annotations...'):
hmm_name = os.path.basename(hmm)
glen = len(genome)
for frame in hmm_results:
for hit in frame:
frec = translation[hit.id]
start = frec.annotations['start']
strand = frec.annotations['strand']
for hsp in hit:
if strand == 1:
hmm_location = FeatureLocation(
start + hsp.hit_start * 3,
start + hsp.hit_end * 3, strand)
else:
hmm_location = FeatureLocation(
glen - start - hsp.hit_end * 3,
glen - start - hsp.hit_start * 3,
strand)
hmm_feature = self.hsp2feature(
hmm_name, 'HMM_annotations', hmm_location,
hsp)
genome.features.append(hmm_feature)
return results if results else None
def blastp_annotate(self, tag_sequences, subject_record, min_identity, evalue=0.001, table=11, **kwargs):
# translate subject in six frames
with user_message('Translating whole genome in 6 reading frames', '\n'):
translator = Translator(self._abort_event)
translation = translator.translate_six_frames(subject_record, table)
if not translation: return False
results = self.s2s_blast_batch(tag_sequences, translation, evalue=evalue, command='blastp', **kwargs)
if results is None: return False
with user_message('Adding results as annotations...'):
annotated = False
subj_len = len(subject_record)
for i, tag in enumerate(tag_sequences):
if not results[i]: continue
tag_name = pretty_rec_name(tag)
if tag_name != tag.id:
tag_name += ' (%s)' % tag.id
for frame, record in enumerate(results[i]):
if not record: continue
frec = translation[frame]
start = frec.annotations['start']
strand = frec.annotations['strand']
for hit in record:
for ali in hit.alignments:
for hsp in ali.hsps:
if hsp.identities / float(hsp.align_length) < min_identity: continue
if strand == 1:
location = FeatureLocation(start+(hsp.sbjct_start-1)*3,
start+hsp.sbjct_end*3,
strand)
else:
location = FeatureLocation(subj_len-start-hsp.sbjct_end*3,
subj_len-start-hsp.sbjct_start*3,
strand)
feature = self.hsp2feature(tag_name, 'blastp_annotations', location, hsp)
self.add_program(feature, 'blastp')
subject_record.features.append(feature)
annotated = True
return annotated
