concord_search.fifth_concordance = return_vals[-9]
return 1
if __name__ == '__main__':
#Handle arguments
parser = argparse.ArgumentParser(description='Puts the project-summary.csv info into the bcbio database')
parser.add_argument('sample_key', type=str, help='The sample name from which the snp_stats process is keyed')
parser.add_argument('-d','--directory', dest='directory', type=str, default=None, help='The path to the concordance and hethom files. The default is the files stored in the snp_stats process.')
parser.add_argument('--search', dest='search', action='store_true', help='This extracts and stores the search statistics instead of the snp_stats statistics.')
args = parser.parse_args()
system_config = ConfigParser.ConfigParser()
system_config.read('/home/sequencing/src/pipeline_project/pipeline/config/ihg_system.cfg')
pipeline_config = ConfigParser.ConfigParser()
pipeline_config.read('/home/sequencing/src/pipeline_project/pipeline/config/qc_on_ihg.cfg')
mockdb = initiate_mockdb(system_config)
sample_snp_stats_dict = mockdb['SnpStats'].__attribute_value_to_object_dict__('sample_key')
try:
snp_stats = sample_snp_stats_dict[args.sample_key][0]
print snp_stats.sample_key + "," + str(snp_stats.key)
except KeyError:
pieces = args.sample_key.split('-')
sample_key2 = pieces[0] + '-' + pieces[1] + '_' + pieces[2]
#sys.stderr.write("%s\n" % sample_key2)
snp_stats = sample_snp_stats_dict[sample_key2][0]
if args.search:
concord_search = mockdb['ConcordanceSearch'].objects[snp_stats.search_key]
store_search_stats_in_db(concord_search,directory=args.directory,sample_key=args.sample_key)
else:
store_snp_stats_in_db(snp_stats,directory=args.directory,sample_key=args.sample_key)
save_mockdb(system_config,mockdb)
#Complete any backup process that have been initiated by a finished sequencing run.
#for pipeline_name in pipeline_config.keys():
# configs.update({'pipeline':pipeline_config[pipeline_name]})
# continue_backup_processes(configs,storage_devices,mockdb)
#Advance the running pipelines. If a step is done, preceed to the next. If the pipeline is done, complete it.
if system_config.get("Logging","debug") is "True":
print "Advancing"
for pipeline_name in pipeline_config.keys():
if system_config.get("Logging","debug") is "True":
print "Advancing " + pipeline_name
if pipeline_name == 'QualityControlPipeline':
configs.update({'pipeline':pipeline_config['QualityControlPipeline']})
advance_running_qc_pipelines(configs,mockdb,storage_devices=storage_devices)
else:
configs.update({'pipeline':pipeline_config[pipeline_name]})
advance_running_std_pipelines(configs,mockdb,pipeline_name,storage_devices=storage_devices)
#The remaining pipeline are taking up storage. I used to account for this, but no longer. This can be added back in, but needs a little work.
#add_running_storage(configs['system'],storage_devices,mockdb)
#If there is enough space, move the next pipeline into the queue
for pipeline_name in pipeline_config:
configs.update({'pipeline':pipeline_config[pipeline_name]})
run_pipelines_with_enough_space(configs,storage_devices,mockdb,pipeline_name)
#Generate and send any outstanding reports.
configs.update({'pipeline':pipeline_config['QualityControlPipeline']})
handle_automated_reports(configs,mockdb)
save_mockdb(configs['system'],mockdb)
for object_key, object in collection.objects.iteritems():
try:
if object.sample_key == orig_sample_key:
object.sample_key = new_sample_key
count += 1
except AttributeError:
pass
return count
def rename_sample_key(config,mockdb,orig_sample_key,new_sample_key):
collection_clses = child_classes(Sample,config=config) + [Sample]
for cls in collection_clses:
collection = mockdb[cls.__name__]
for object_key, object in collection.objects.iteritems():
if object.key == orig_sample_key:
object.key = new_sample_key
return 1
if __name__ == '__main__':
#Handle arguments
parser = argparse.ArgumentParser(description='Puts the project-summary.csv info into the bcbio database')
parser.add_argument('sample_key', type=str, help='The sample name as it currently is in the database')
parser.add_argument('new_key', type=str, help='The sample name to which the sample_key will be renamed')
args = parser.parse_args()
config = ConfigParser.ConfigParser()
config.read('/home/sequencing/src/pipeline_project/pipeline/config/qc_on_ihg.cfg')
mockdb = initiate_mockdb(config)
rename_all_sample_keys(mockdb,args.sample_key,args.new_key)
rename_sample_key(config,mockdb,args.sample_key,args.new_key)
save_mockdb(config,mockdb)
