def __init__(self, callback, database, queries, blast_version='blastx') :
super(BlastJob, self).__init__(callback)
self.database = database
self.queries = queries
assert blast_version in ('blastx', 'tblastx')
self.blastx = Tblastx() if blast_version == 'tblastx' else Blastx()
class BlastJob(Job) :
def __init__(self, callback, database, queries, blast_version='blastx') :
super(BlastJob, self).__init__(callback)
self.database = database
self.queries = queries
assert blast_version in ('blastx', 'tblastx')
self.blastx = Tblastx() if blast_version == 'tblastx' else Blastx()
@property
def input(self) :
return self.queries
@property
def results(self) :
return self.blastx.results
def _get_filenames(self) :
return [self.query_fname, self.out_fname]
def _run(self) :
global DEBUG
self.query_fname = tmpfasta(self.queries)
self.out_fname = tmpfile()
result = self.blastx.run(self.query_fname, self.database, self.out_fname)
q = dict([ (q.id, len(q)) for q in self.input ])
if DEBUG :
for br in self.results :
threadsafe_io('blastx_stats.txt', "%s %s %.3f %d %d %d %d %d %.3e %d %.3f" % \
(br.qseqid,
br.sseqid,
br.pident,
br.length,
br.qstart,
br.qend,
br.sstart,
br.send,
br.evalue,
q[br.qseqid],
((br.pident / 100.0) * (max(br.qstart, br.qend) - min(br.qstart, br.qend))) / float(q[br.qseqid])))
return result
