def chimera(runobj):
chimera_cluster_ids = []
logger.debug("Starting Chimera Checker")
# lets read the trim status file out here and keep those details out of the Chimera code
idx_keys = get_keys(runobj)
#new_lane_keys = convert_unicode_dictionary_to_str(json.loads(open(runobj.trim_status_file_name,"r").read()))["new_lane_keys"]
# Open run STATUS File here.
# open in append mode because we may start the run in the middle
# say at the gast stage and don't want to over write.
# if we re-run trimming we'll get two trim status reports
runobj.run_status_file_h = open(runobj.run_status_file_name, "a")
mychimera = Chimera(runobj)
logger.debug("\nStarting DeNovo Chimera")
c_den = mychimera.chimera_denovo()
logger.debug("Ending DeNovo Chimera")
if c_den[0] == 'SUCCESS':
chimera_cluster_ids += c_den[2] # add a list to a list
logger.debug("chimera_cluster_ids: "+' '.join(chimera_cluster_ids))
chimera_code='PASS'
elif c_den[0] == 'NOREGION':
chimera_code='NOREGION'
elif c_den[0] == 'FAIL':
chimera_code = 'FAIL'
else:
chimera_code='FAIL'
logger.debug("Chimera DeNovo Code: "+chimera_code)
logger.debug("\nStarting Reference Chimera")
c_ref = mychimera.chimera_reference()
if c_ref[0] == 'SUCCESS':
chimera_cluster_ids += c_ref[2]
chimera_code='PASS'
elif c_ref[0] == 'NOREGION':
chimera_code = 'NOREGION'
elif c_ref[0] == 'FAIL':
chimera_code='FAIL'
else:
chimera_code='FAIL'
#print chimera_cluster_ids
runobj.chimera_status_file_h = open(runobj.chimera_status_file_name,"w")
if chimera_code == 'PASS':
if runobj.use_cluster:
chimera_cluster_code = wait_for_cluster_to_finish(chimera_cluster_ids)
if chimera_cluster_code[0] == 'SUCCESS':
logger.info("Chimera checking finished successfully")
runobj.chimera_status_file_h.write("CHIMERA SUCCESS\n")
runobj.run_status_file_h.write("CHIMERA SUCCESS\n")
else:
logger.info("3-Chimera checking Failed")
runobj.chimera_status_file_h.write("3-CHIMERA ERROR: "+str(chimera_cluster_code[1])+" "+str(chimera_cluster_code[2])+"\n")
runobj.run_status_file_h.write("3-CHIMERA ERROR: "+str(chimera_cluster_code[1])+" "+str(chimera_cluster_code[2])+"\n")
sys.exit("3-Chimera checking Failed")
else:
chimera_cluster_code = ['SUCCESS','Not using cluster']
logger.info("Chimera checking finished without using cluster")
runobj.chimera_status_file_h.write("CHIMERA SUCCESS--no cluster\n")
runobj.run_status_file_h.write("CHIMERA SUCCESS--no cluster\n")
elif chimera_code == 'NOREGION':
logger.info("No regions found that need chimera checking")
runobj.chimera_status_file_h.write("CHIMERA CHECK NOT NEEDED\n")
runobj.run_status_file_h.write("CHIMERA CHECK NOT NEEDED\n")
elif chimera_code == 'FAIL':
logger.info("1-Chimera checking Failed")
runobj.chimera_status_file_h.write("1-CHIMERA ERROR: \n")
runobj.run_status_file_h.write("1-CHIMERA ERROR: \n")
sys.exit("1-Chimera Failed")
else:
logger.info("2-Chimera checking Failed")
runobj.chimera_status_file_h.write("2-CHIMERA ERROR: \n")
runobj.run_status_file_h.write("2-CHIMERA ERROR: \n")
sys.exit("2-Chimera checking Failed")
sleep(2)
if chimera_code == 'PASS' and chimera_cluster_code[0] == 'SUCCESS':
logger.info("Writing Chimeras to deleted files")
mychimera.write_chimeras_to_deleted_file()
# should also recreate fasta
# then read chimera files and place (or replace) any chimeric read_id
# into the deleted file.
mymblutils = MBLPipelineFastaUtils(idx_keys, runobj)
# write new cleaned files that remove chimera if apropriate
# these are in fasta_mbl_pipeline.py
# the cleaned file are renamed to the original name:
# lane_key.unique.fa
# lane_key.trimmed.fa
# lane_key.names --
# lane_key.abund.fa -- this file is for the uclust chimera script
# lane_key.deleted.txt -- no change in this file
# THE ORDER IS IMPORTANT HERE:
mymblutils.write_clean_fasta_file()
mymblutils.write_clean_names_file()
mymblutils.write_clean_uniques_file()
mymblutils.write_clean_abundance_file()
def chimera(runobj):
chimera_cluster_ids = []
logger.debug("Starting Chimera Checker")
# lets read the trim status file out here and keep those details out of the Chimera code
idx_keys = get_keys(runobj)
#new_lane_keys = convert_unicode_dictionary_to_str(json.loads(open(runobj.trim_status_file_name,"r").read()))["new_lane_keys"]
mychimera = Chimera(runobj)
c_den = mychimera.chimera_denovo(idx_keys)
if c_den[0] == 'SUCCESS':
chimera_cluster_ids += c_den[2]
chimera_code='PASS'
elif c_den[0] == 'NOREGION':
chimera_code='NOREGION'
elif c_den[0] == 'FAIL':
chimera_code = 'FAIL'
else:
chimera_code='FAIL'
c_ref = mychimera.chimera_reference(idx_keys)
if c_ref[0] == 'SUCCESS':
chimera_cluster_ids += c_ref[2]
chimera_code='PASS'
elif c_ref[0] == 'NOREGION':
chimera_code = 'NOREGION'
elif c_ref[0] == 'FAIL':
chimera_code='FAIL'
else:
chimera_code='FAIL'
#print chimera_cluster_ids
runobj.chimera_status_file_h = open(runobj.chimera_status_file_name,"w")
if chimera_code == 'PASS':
chimera_cluster_code = wait_for_cluster_to_finish(chimera_cluster_ids)
if chimera_cluster_code[0] == 'SUCCESS':
logger.info("Chimera checking finished successfully")
runobj.chimera_status_file_h.write("CHIMERA SUCCESS\n")
runobj.run_status_file_h.write("CHIMERA SUCCESS\n")
else:
logger.info("3-Chimera checking Failed")
runobj.chimera_status_file_h.write("3-CHIMERA ERROR: "+str(chimera_cluster_code[1])+" "+str(chimera_cluster_code[2])+"\n")
runobj.run_status_file_h.write("3-CHIMERA ERROR: "+str(chimera_cluster_code[1])+" "+str(chimera_cluster_code[2])+"\n")
sys.exit("3-Chimera checking Failed")
elif chimera_code == 'NOREGION':
logger.info("No regions found that need chimera checking")
runobj.chimera_status_file_h.write("CHIMERA CHECK NOT NEEDED\n")
runobj.run_status_file_h.write("CHIMERA CHECK NOT NEEDED\n")
elif chimera_code == 'FAIL':
logger.info("1-Chimera checking Failed")
runobj.chimera_status_file_h.write("1-CHIMERA ERROR: \n")
runobj.run_status_file_h.write("1-CHIMERA ERROR: \n")
sys.exit("1-Chimera Failed")
else:
logger.info("2-Chimera checking Failed")
runobj.chimera_status_file_h.write("2-CHIMERA ERROR: \n")
runobj.run_status_file_h.write("2-CHIMERA ERROR: \n")
sys.exit("2-Chimera checking Failed")
sleep(2)
if chimera_code == 'PASS' and chimera_cluster_code[0] == 'SUCCESS':
mychimera.write_chimeras_to_deleted_file(idx_keys)
# should also recreate fasta
# then read chimera files and place (or replace) any chimeric read_id
# into the deleted file.
mymblutils = MBLPipelineFastaUtils(idx_keys, mychimera.outdir)
# write new cleaned files that remove chimera if apropriate
# these are in fasta_mbl_pipeline.py
# the cleaned file are renamed to the original name:
# lane_key.unique.fa
# lane_key.trimmed.fa
# lane_key.names --
# lane_key.abund.fa -- this file is for the uclust chimera script
# lane_key.deleted.txt -- no change in this file
# THE ORDER IS IMPORTANT HERE:
mymblutils.write_clean_fasta_file()
mymblutils.write_clean_names_file()
mymblutils.write_clean_uniques_file()
mymblutils.write_clean_abundance_file()
# write keys file for each lane_key - same fields as db table? for easy writing
# write primers file for each lane_key
# Write new clean files to the database
# rawseq table not used
# trimseq
# runkeys
# primers
# run primers
mymblutils.write_clean_files_to_database()
def chimera(runobj):
chimera_cluster_ids = []
logger.debug("Starting Chimera Checker")
# lets read the trim status file out here and keep those details out of the Chimera code
idx_keys = get_keys(runobj)
# new_lane_keys = convert_unicode_dictionary_to_str(json.loads(open(runobj.trim_status_file_name,"r").read()))["new_lane_keys"]
# Open run STATUS File here.
# open in append mode because we may start the run in the middle
# say at the gast stage and don't want to over write.
# if we re-run trimming we'll get two trim status reports
runobj.run_status_file_h = open(runobj.run_status_file_name, "a")
mychimera = Chimera(runobj)
logger.debug("\nStarting DeNovo Chimera")
c_den = mychimera.chimera_denovo()
logger.debug("Ending DeNovo Chimera")
if c_den[0] == 'SUCCESS':
chimera_cluster_ids += c_den[2] # add a list to a list
logger.debug("chimera_cluster_ids: " + ' '.join(chimera_cluster_ids))
chimera_code = 'PASS'
elif c_den[0] == 'NOREGION':
chimera_code = 'NOREGION'
elif c_den[0] == 'FAIL':
chimera_code = 'FAIL'
else:
chimera_code = 'FAIL'
logger.debug("Chimera DeNovo Code: " + chimera_code)
logger.debug("\nStarting Reference Chimera")
c_ref = mychimera.chimera_reference()
if c_ref[0] == 'SUCCESS':
chimera_cluster_ids += c_ref[2]
chimera_code = 'PASS'
elif c_ref[0] == 'NOREGION':
chimera_code = 'NOREGION'
elif c_ref[0] == 'FAIL':
chimera_code = 'FAIL'
else:
chimera_code = 'FAIL'
# logger.debug(chimera_cluster_ids)
runobj.chimera_status_file_h = open(runobj.chimera_status_file_name, "w")
if chimera_code == 'PASS':
if runobj.use_cluster:
chimera_cluster_code = wait_for_cluster_to_finish(
chimera_cluster_ids)
if chimera_cluster_code[0] == 'SUCCESS':
logger.info("Chimera checking finished successfully")
runobj.chimera_status_file_h.write("CHIMERA SUCCESS\n")
runobj.run_status_file_h.write("CHIMERA SUCCESS\n")
else:
logger.info("3-Chimera checking Failed")
runobj.chimera_status_file_h.write(
"3-CHIMERA ERROR: " + str(chimera_cluster_code[1]) + " " +
str(chimera_cluster_code[2]) + "\n")
runobj.run_status_file_h.write("3-CHIMERA ERROR: " +
str(chimera_cluster_code[1]) +
" " +
str(chimera_cluster_code[2]) +
"\n")
sys.exit("3-Chimera checking Failed")
else:
chimera_cluster_code = ['SUCCESS', 'Not using cluster']
logger.info("Chimera checking finished without using cluster")
runobj.chimera_status_file_h.write("CHIMERA SUCCESS--no cluster\n")
runobj.run_status_file_h.write("CHIMERA SUCCESS--no cluster\n")
elif chimera_code == 'NOREGION':
logger.info("No regions found that need chimera checking")
runobj.chimera_status_file_h.write("CHIMERA CHECK NOT NEEDED\n")
runobj.run_status_file_h.write("CHIMERA CHECK NOT NEEDED\n")
elif chimera_code == 'FAIL':
logger.info("1-Chimera checking Failed")
runobj.chimera_status_file_h.write("1-CHIMERA ERROR: \n")
runobj.run_status_file_h.write("1-CHIMERA ERROR: \n")
sys.exit("1-Chimera Failed")
else:
logger.info("2-Chimera checking Failed")
runobj.chimera_status_file_h.write("2-CHIMERA ERROR: \n")
runobj.run_status_file_h.write("2-CHIMERA ERROR: \n")
sys.exit("2-Chimera checking Failed")
sleep(2)
if chimera_code == 'PASS' and chimera_cluster_code[0] == 'SUCCESS':
logger.info("Writing Chimeras to deleted files")
mychimera.write_chimeras_to_deleted_file()
# should also recreate fasta
# then read chimera files and place (or replace) any chimeric read_id
# into the deleted file.
mymblutils = MBLPipelineFastaUtils(idx_keys, runobj)
# write new cleaned files that remove chimera if apropriate
# these are in fasta_mbl_pipeline.py
# the cleaned file are renamed to the original name:
# lane_key.unique.fa
# lane_key.trimmed.fa
# lane_key.names --
# lane_key.abund.fa -- this file is for the uclust chimera script
# lane_key.deleted.txt -- no change in this file
# THE ORDER IS IMPORTANT HERE:
mymblutils.write_clean_fasta_file()
mymblutils.write_clean_names_file()
mymblutils.write_clean_uniques_file()
mymblutils.write_clean_abundance_file()