class PrankJob(Job) :
def __init__(self, callback, sequences) :
super(PrankJob, self).__init__(callback)
self.sequences = sequences
self.prank = Prank()
@property
def input(self) :
return self.sequences
@property
def tree(self) :
return self.prank.tree
@property
def alignment(self) :
return self.prank.alignment
def _get_filenames(self) :
return [self.infile] + self.prank.output_filenames(self.infile)
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
def __init__(self, callback, sequences) :
super(PrankJob, self).__init__(callback)
self.sequences = sequences
self.prank = Prank()
