def hmmsearch_genes(self,
hmms,
genome,
table='Standard',
decorate=False,
**kwargs):
#get _genes
genes = get_indexes_of_all_genes(genome)
if not genes: return None
for gene_id, gi in enumerate(genes):
genome.features[gi].qualifiers['feature_id'] = gi
genome.features[gi].qualifiers['gene_id'] = gene_id
#translate _genes
with user_message('Translating _genes/CDS of %s' % genome.description,
'\n'):
translator = Translator(self._abort_event)
translation = translator.translate_features(genome, genes, table)
if not translation: return None
if isinstance(hmms, str): hmms = [hmms]
results = dict()
for hmm in hmms:
with user_message('Performing hmm search.'):
hmm_results = self.hmmsearch_recs(hmm, translation, **kwargs)
if not hmm_results: return None
with user_message('Parsing search results...'):
#get hit_ids of hmm matches
hits = dict()
for result in hmm_results:
for hit in result.iterhits():
hits[hit.id] = hit
#get indexes of features where hmm hit
hit_features = dict()
for t in translation:
if t.id in hits:
fid = t.features[0].qualifiers.get('feature_id')
if fid is None: continue
hit_features[fid] = hits[t.id], t
if hit_features: results.update(hit_features)
#decorate genome
if decorate:
with user_message('Adding results as annotations...'):
hmm_name = os.path.basename(hmm)
for f in hit_features:
feature = genome.features[f]
for hsp in hit_features[f][0]:
if feature.strand == 1:
hmm_location = FeatureLocation(
feature.location.start + hsp.hit_start * 3,
feature.location.start + hsp.hit_end * 3,
feature.strand)
else:
hmm_location = FeatureLocation(
feature.location.end - hsp.hit_end * 3,
feature.location.end - hsp.hit_start * 3,
feature.strand)
hmm_feature = self.hsp2feature(
hmm_name, 'HMM_annotations', hmm_location, hsp)
genome.features.append(hmm_feature)
return results if results else None
def g2g_blastp(self, reference, subjects, table='Standard',
evalue=0.001, max_rlen=0, features_of_interest=None):
'''
Perform blastp of each coding sequence of the reference against each
subject, which is first translated gene-by-gene.
Parameters
@param reference: SeqRecord object of the reference genome
@param subjects: a list of SeqRecord objects of subject genomes
@param table: translation table number (see NCBI site for description)
@param evalue: filter out blastp results with E-value grater than this
@param max_rlen: filter out blastp results which are shorter than this
fraction of target gene length
@param features_of_interest: list of dictionaries of the form
{qualifier_name : qualifier_value}
to mark features denoting known clusters that should be analyzed one
against the other
@return: list of pairs (CDS, (blast_result1, blast_result2, ...))
where CDS is a gene/CDS feature from the reference.features list
and blast_resultN is a list of results for the N-th
subject, containing following information:
(hit_feature, align_length, percent_identity, evalue)
where hit_feature is a SeqFeature object of the gene/CDS of the subject
where top blast hit is located, align_length is the length of the hit,
percent_identity is the ratio of number of identities and align_length [0; 1]
and evalue is the E-value of the top hit.
'''
if not reference or not subjects:
print 'No reference or subject sequences provided'
return None
#get list of features to query
with user_message('Searching for gene/CDS features in provided sequences...'):
all_records = [reference]+subjects
num_records = len(all_records)
features = self.parallelize_work(1, lambda ri, records: self._get_genes(records[ri]),
range(num_records),
all_records)
if self.aborted():
print '\nAborted'
return None
if not features or not features[0]:
print ('\nReference sequence does not contain annotated _genes:\n%s %s'
% (reference.id, reference.description))
return None
if len([f for f in features if f]) < 2:
print '\nSubject sequences do not contain annotated _genes'
return None
#add gene ids
for ri, genes in enumerate(features):
if not genes: continue
r = all_records[ri]
for gene_id, gi in enumerate(genes):
r.features[gi].qualifiers['feature_id'] = gi
r.features[gi].qualifiers['gene_id'] = gene_id
#get features of interest if requested
fois = None
if features_of_interest:
with user_message('Searching for features of interest...'):
fois = []
for foi in features_of_interest:
foi = self._get_fois(all_records, foi)
if foi and foi[0]: fois.append(foi)
if self.aborted():
print '\nAborted'
return None
#translate features to proteins
with Progress('Translating _genes found in the reference and subjects...', num_records) as prg:
translator = Translator(self._abort_event)
translations = [None]*num_records
foi_translations = [[None]*num_records for _f in fois]
for i, (f, rec) in enumerate(zip(features, all_records)):
if not f:
prg.step(i)
continue
translation = translator.translate_features(rec, f, table)
if not translation: return None
if i > 0:
translations[i] = cat_records(translation)
if fois:
for ifoi, foi in enumerate(fois):
foi_loc = [0, 0]
for foi_var in foi[i]:
if not foi_var: continue
for gid in foi_var:
l = translations[i].features[gid].location
foi_loc[0] = min(int(l.start)+1, foi_loc[0]) if foi_loc[0] > 0 else int(l.start)+1
foi_loc[1] = max(int(l.end), foi_loc[1])
if foi_loc[0] > 0: foi_translations[ifoi][i] = foi_loc
else:
translations[i] = translation
if fois:
for ifoi, foi in enumerate(fois):
foi_translations[ifoi][i] = [[translation[gid] for gid in foi_var] for foi_var in foi[i]]
prg.step(i)
#blast features against subjects
with user_message('Performing local blast of every translated gene in the reference against every translated subject...', '\n'):
stranslations = translations[1:]
blast_results = self._s2s_blast_batch(translations[0], stranslations, None, evalue,
command='blastp', task='blastp')
if self.aborted():
print '\nAborted'
return None
if not blast_results:
print '\nBlast have not returned any results.'
return None
if fois: #redo blast for fois and replace the results
with user_message('Rerunning blast for FOIs...', '\n'):
for ifoi, foi in enumerate(foi_translations):
sfoi_locs = foi[1:]
for i, foi_var in enumerate(foi[0]):
foi_blast = self._s2s_blast_batch(foi_var, stranslations, sfoi_locs, evalue,
command='blastp', task='blastp')
if self.aborted():
print '\nAborted'
return None
if not foi_blast: continue
for gi, gid in enumerate(fois[ifoi][0][i]):
if foi_blast[gi]:
blast_results[gid] = foi_blast[gi]
#process blast results
pairs = list(itertools.product(xrange(len(translations[0])), xrange(len(stranslations))))
with ProgressCounter('Searching for _genes in subjects that overlap with top blast hits...', len(pairs)) as prg:
work = self.Work()
work.start_work(self._find_features_by_hsps, pairs,
None, stranslations, blast_results)
@MultiprocessingBase.results_assembler
def assembler(index, result, blast_results, pairs, prg):
qs = pairs[index]
blast_results[qs[0]][qs[1]] = result
prg.count()
work.assemble(assembler, blast_results, pairs, prg)
if not work.wait(): return None
return zip((reference.features[f] for f in features[0]), blast_results)
