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