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))
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)