def __init__(self, callback, queries, genefamily_id, alignment, tree, identity, overlap) :
super(PaganJob, self).__init__(callback)
self._queries = queries
self._genefamily = genefamily_id
self._alignment = alignment
self._tree = tree
self.identity = identity
self.overlap = overlap
self.pagan = Pagan()
self.query_fname = None
self.out_fname = None
self.alignment_fname = None
self.tree_fname = None
class PaganJob(Job) :
def __init__(self, callback, queries, genefamily_id, alignment, tree, identity, overlap) :
super(PaganJob, self).__init__(callback)
self._queries = queries
self._genefamily = genefamily_id
self._alignment = alignment
self._tree = tree
self.identity = identity
self.overlap = overlap
self.pagan = Pagan()
self.query_fname = None
self.out_fname = None
self.alignment_fname = None
self.tree_fname = None
@property
def input(self) :
return self._queries
@property
def genefamily(self) :
return self._genefamily
@property
def nucleotide_alignment(self) :
return self.pagan.nucleotide_alignment
@property
def protein_alignment(self) :
return self.pagan.protein_alignment
def _get_filenames(self) :
#return self.pagan.output_filenames(self.out_fname)
return [self.query_fname, self.alignment_fname, self.tree_fname] + self.pagan.output_filenames(self.out_fname)
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