def illumina_chimera_after_cluster(runobj):
mychimera = Chimera(runobj)
mychimera.illumina_rm_size_files()
start = time.time()
mychimera.illumina_size_to_freq_in_chimer()
elapsed = (time.time() - start)
print "illumina_size_to_freq_in_chimer time: %s" % elapsed
# start = time.time()
# print "Check chimeric statistics. If ref > 15% and ratio ref to de-novo > 2 use only de-novo"
# mychimera.check_chimeric_stats()
# elapsed = (time.time() - start)
# print "check_chimeric_stats time: %s" % elapsed
start = time.time()
print "Creating nonchimeric files in %s" % mychimera.indir
mychimera.move_out_chimeric()
elapsed = (time.time() - start)
print "move_out_chimeric time: %s" % elapsed
print "illumina_chimera_after_cluster time = %s" % str(elapsed)
def illumina_chimera_after_cluster(runobj):
mychimera = Chimera(runobj)
mychimera.illumina_rm_size_files()
start = time.time()
mychimera.illumina_size_to_freq_in_chimer()
elapsed = (time.time() - start)
logger.debug("illumina_size_to_freq_in_chimer time: %s" % elapsed)
# start = time.time()
# logger.debug("Check chimeric statistics. If ref > 15% and ratio ref to de-novo > 2 use only de-novo")
# mychimera.check_chimeric_stats()
# elapsed = (time.time() - start)
# logger.debug("check_chimeric_stats time: %s" % elapsed)
start = time.time()
logger.debug("Creating nonchimeric files in %s" % mychimera.indir)
mychimera.move_out_chimeric()
elapsed = (time.time() - start)
logger.debug("move_out_chimeric time: %s" % elapsed)
logger.debug("illumina_chimera_after_cluster time = %s" % str(elapsed))
