class All_vs_all_search(object):
def __init__(self, batch_size=100):
self.nucleotide = False
self.min_hitidentity = None
self.min_hitlength = None
self.max_evalue = None
self.batch_size = batch_size
self.log = get_log()
self.cleanup_files = []
self.gene_assignments = {}
self.lock = threading.Lock()
self.q = None
self.total_jobs = 0
self.complete_jobs = 0
def _batch(self, x):
tmp = []
for i in x:
tmp.append(i)
if len(tmp) == self.batch_size:
yield tmp
tmp = []
if not tmp:
raise StopIteration
yield tmp
def process(self, db, queries, nucleotide, min_hitidentity, min_hitlength, max_evalue):
self.nucleotide = nucleotide
self.min_hitidentity = min_hitidentity
self.min_hitlength = min_hitlength
self.max_evalue = max_evalue
# we need to deal with the index files here because
# all of the blastx jobs need them
self.cleanup_files += [db + i for i in [".phr", ".pin", ".psq"]]
# creates db + {phr,pin,psq} in same dir as db
self.log.info("creating blast db...")
Blast.makedb(db) # XXX THIS IS ALWAYS PROTEIN, BECAUSE WE WANT TO RUN BLASTX
# queue up the jobs
self.log.info("starting local alignments...")
self.q = WorkQueue()
self.total_jobs = len(queries)
self.complete_jobs = -self.batch_size
self._progress()
for query in self._batch(queries):
self.q.enqueue(BlastJob(self.job_callback, db, query, "blastx"))
self.log.debug("waiting for job queue to drain...")
self.q.join()
rm_f(self.cleanup_files)
return self.gene_assignments
def stop(self):
if self.q:
self.q.stop()
rm_f(self.cleanup_files)
def get_intermediate_results(self):
return self.gene_assignments
def _progress(self):
self.complete_jobs += self.batch_size
if self.complete_jobs > self.total_jobs:
self.complete_jobs = self.total_jobs
sys.stderr.write("\rProgress: %d / %d blastx alignments " % (self.complete_jobs, self.total_jobs))
if self.complete_jobs == self.total_jobs:
sys.stderr.write("\n")
sys.stderr.flush()
def job_callback(self, job):
self.log.debug("%d blast results returned" % len(job.results))
self.lock.acquire()
self._progress()
if job.success():
qlen = dict([(q.id, len(q)) for q in job.input])
for br in job.results:
# length = max(br.qstart, br.qend) - min(br.qstart, br.qend)
strand = "+" if br.qstart < br.qend else "-"
if (
(br.qseqid in self.gene_assignments)
or (self.max_evalue < br.evalue)
or (self.min_hitidentity > br.pident)
or (self.min_hitlength > br.length)
):
continue
self.gene_assignments[br.qseqid] = (br.sseqid, strand)
for q in job.input:
if q.id not in self.gene_assignments:
self.gene_assignments[q.id] = None
self.lock.release()
