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
def _run(self) :
global DEBUG
self.query_fname = tmpfasta_orfs(self._queries, strand=True)
#self.query_fname = tmpfasta(self._queries)
self.out_fname = tmpfile()
self.alignment_fname = tmpfasta(self._alignment) # tmpfasta_kill_n(self._alignment)
self.tree_fname = tmpfile(self._tree) if self._tree else None
start_time = time.time()
result = self.pagan.run(self.query_fname,
self.out_fname,
self.alignment_fname,
self.tree_fname,
self.identity,
self.overlap)
elapsed_time = time.time() - start_time
q_count, q_sum, q_min, q_max, q_mean, q_sd = fasta_stats(self.query_fname)
a_count, a_sum, a_min, a_max, a_mean, a_sd = fasta_stats(self.alignment_fname)
if DEBUG :
threadsafe_io('pagan_stats.txt', "%s %d %d %d %d %d %.3f %.3f %d %d %d %d %.3f %.3f %d" % \
(self._genefamily, result, \
q_count, q_sum, q_min, q_max, q_mean, q_sd, \
a_count, a_sum, a_min, a_max, a_mean, a_sd, \
elapsed_time))
return result
def _run(self) :
global DEBUG
self.infile = tmpfasta(self.sequences)
start_time = time.time()
result = self.prank.run(self.infile, self.infile)
elapsed_time = time.time() - start_time
q_count, q_sum, q_min, q_max, q_mean, q_sd = fasta_stats(self.infile)
if DEBUG :
threadsafe_io('prank_stats.txt', "%d %d %d %d %d %.3f %.3f %d" % \
(result, \
q_count, q_sum, q_min, q_max, q_mean, q_sd, \
elapsed_time))
return result
