def illumina_chimera(runobj):
utils = PipelneUtils()
start = time.time()
mychimera = Chimera(runobj)
# elapsed = (time.time() - start)
# print elapsed
print "Preparing input files (replacing \"frequency:\" with \";size=\" and capitalize reads)"
# start = time.time()
# mychimera.illumina_freq_to_size_in_chg()
# elapsed = (time.time() - start)
# print "1a) illumina_freq_to_size_in_chg time: %s" % elapsed
start = time.time()
mychimera.call_illumina_sed("from_frequency_to_size")
elapsed = (time.time() - start)
print "call_illumina_sed from_frequency_to_size time: %s" % elapsed
#
print "START chimera checking"
# c_den =
mychimera.chimera_checking("denovo")
# # print "c_den - check denovo res: %s" % c_den
# print c_den
# c_den =
mychimera.chimera_checking("ref")
# print c_den
# todo: use run_until_done_on_cluster from utils
"""run after cluster is done with it work:"""
start = time.time()
time_before = utils.get_time_now()
print "time_before = %s" % time_before
print "Waiting for the cluster..."
while True:
if utils.is_local():
sleep(1)
else:
sleep(120)
cluster_done = mychimera.check_if_cluster_is_done(time_before)
print "cluster_done = %s" % cluster_done
if (cluster_done):
break
elapsed = (time.time() - start)
print "Cluster is done with both chimera checkings in: %s" % elapsed
mychimera.check_if_chimera_dir_empty()
mychimera.illumina_rm_size_files()
# start = time.time()
# mychimera.illumina_size_to_freq_in_chimer()
# elapsed = (time.time() - start)
# print "2a) illumina_size_to_freq_in_chimer time: %s" % elapsed
start = time.time()
mychimera.call_illumina_sed("from_size_to_frequency")
elapsed = (time.time() - start)
print "call_illumina_sed from_size_to_frequency 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
def illumina_chimera(runobj):
utils = PipelneUtils()
# start = time.time()
mychimera = Chimera(runobj)
# elapsed = (time.time() - start)
# logger.debug(elapsed)
logger.debug(
"Preparing input files (replacing \"frequency:\" with \";size=\" and capitalize reads)"
)
# start = time.time()
# mychimera.illumina_freq_to_size_in_chg()
# elapsed = (time.time() - start)
# logger.debug("1a) illumina_freq_to_size_in_chg time: %s" % elapsed)
start = time.time()
mychimera.call_illumina_sed("from_frequency_to_size")
elapsed = (time.time() - start)
logger.debug("call_illumina_sed from_frequency_to_size time: %s" % elapsed)
#
logger.debug("START chimera checking")
# c_den =
mychimera.chimera_checking()
# # logger.debug("c_den - check denovo res: %s" % c_den)
# logger.debug(c_den)
# c_den =
# mychimera.chimera_checking("ref")
# logger.debug(c_den)
# todo: use run_until_done_on_cluster from utils
"""run after cluster is done with it work:"""
start = time.time()
time_before = utils.get_time_now()
logger.debug("time_before = %s" % time_before)
logger.debug("Waiting for the cluster...")
while True:
if utils.is_local():
sleep(1)
break
else:
sleep(120)
cluster_done = mychimera.check_if_cluster_is_done(time_before)
logger.debug("cluster_done = %s" % cluster_done)
if cluster_done:
break
elapsed = (time.time() - start)
logger.debug("Cluster is done with both chimera checkings in: %s" %
elapsed)
mychimera.check_if_chimera_dir_empty()
mychimera.illumina_rm_size_files()
# start = time.time()
# mychimera.illumina_size_to_freq_in_chimer()
# elapsed = (time.time() - start)
# logger.debug("2a) illumina_size_to_freq_in_chimer time: %s" % elapsed)
start = time.time()
mychimera.call_illumina_sed("from_size_to_frequency")
elapsed = (time.time() - start)
logger.debug("call_illumina_sed from_size_to_frequency 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)
