def __init__(self,config,sample_keys=None,number=None,key=int(-1),flowcell=None,input_dir=None,base_output_dir=None,output_dir=None,date=strftime("%Y%m%d",localtime()),time=strftime("%H:%M:%S",localtime()),process_name='flowcell_report',complete_file=None,**kwargs):
"""
Initializes flowcell statistic report.
"""
if flowcell is None:
flowcell = Flowcell(config,key="dummy_flowcell_key")
if flowcell.__class__.__name__ != "Flowcell":
raise Exception("Trying to start a flowcell statistics reports object on a non-flowcell.")
if output_dir is None:
if base_output_dir is None:
base_output_dir = config.get('Common_directories','flowcell_reports')
self.output_dir = os.path.join(os.path.join(base_output_dir,flowcell.key + "_reports"),str(number))
else:
self.output_dir = output_dir
if complete_file is None:
self.complete_file = os.path.join(self.output_dir,"report_" + str(number) + ".complete")
else:
self.complete_file = complete_file
QsubProcess.__init__(self,config,key=key,input_dir=input_dir,base_output_dir=base_output_dir,output_dir=self.output_dir,date=date,time=time,process_name=process_name,complete_file=self.complete_file,**kwargs)
self.flowcell_key = flowcell.key
if sample_keys is None:
self.sample_keys = ""
else:
self.sample_keys = ";".join(sample_keys)
self.number = number
#List of samples from the project
self.all_samples_file = os.path.join(self.output_dir,'all_samples.ls')
if self.key != -1:
write_list_file(sample_keys,self.all_samples_file,original_list_file=config.get('Filenames','all_samples'))
self.current_samples_file = os.path.join(self.output_dir,'current_samples.ls')
if self.key != -1:
write_list_file(sample_keys,self.current_samples_file)
#Output files
self.full_report = os.path.join(self.output_dir,'all_samples_report.csv')
self.current_report = os.path.join(self.output_dir,'current_samples_report.csv')
self.concordance_jpeg = os.path.join(self.output_dir,'concordance_vs_depth.jpeg')
self.dbsnp_jpeg = os.path.join(self.output_dir,'dbsnp_vs_depth.jpeg')
self.greater_than_10x_jpeg = os.path.join(self.output_dir,'greater_than_10x_vs_depth.jpeg')
self.zero_coverage_jpeg = os.path.join(self.output_dir,'zero_coverage_vs_depth.jpeg')
self.hethomratio_jpeg = os.path.join(self.output_dir,'hethomratio_vs_depth.jpeg')
self.reads_jpeg = os.path.join(self.output_dir,'reads_vs_depth.jpeg')
self.report_pdf = os.path.join(self.output_dir,self.flowcell_key + '_report.pdf')
#Flag to keep track if report has been sent
self.report_sent = False
def __send_reports__(self,config,mockdb):
"""
For reports that have generated but not been sent,
this script attaches the appropriate plots and tables
and sends the email.
"""
numbers = config.get('Flowcell_reports','numbers').split(',')
for number in numbers:
flowcell_report_key = getattr(self,'flowcell_report_' + str(number) + '_key')
if flowcell_report_key is None:
continue
report = mockdb['FlowcellStatisticReport'].objects[flowcell_report_key]
if report.report_sent is True: #If the report is already sent, next.
continue
if not report.__is_complete__(): #If the qsub script is still running, next.
continue
if self.sequencing_run_type == 'RapidRun' and str(number) == '16':
recipients = config.get('Flowcell_reports','last_recipients')
subject, body = report.__generate_flowcell_report_text__(config,mockdb,report_type="last_report")
#Add samples to the all sample list
sample_keys = self.__completed_samples_list__(mockdb)
write_list_file(sample_keys,config.get('Filenames','all_samples'),original_list_file=config.get('Filenames','all_samples'))
self.__finish__()
elif self.sequencing_run_type == 'HighThroughputRun' and str(number) == '64':
recipients = config.get('Flowcell_reports','last_recipients')
subject, body = report.__generate_flowcell_report_text__(config,mockdb,report_type="last_report")
#Add samples to the all sample list
sample_keys = self.__completed_samples_list__(mockdb)
write_list_file(sample_keys,config.get('Filenames','all_samples'),original_list_file=config.get('Filenames','all_samples'))
self.__finish__()
else:
recipients = config.get('Flowcell_reports','subset_recipients')
subject, body = report.__generate_flowcell_report_text__(config,mockdb,report_type="subset_report")
files = []
files.append(report.report_pdf)
files.append(report.full_report)
files.append(report.current_report)
send_email(subject,body,recipients=recipients,files=files)
report.__finish__()
report.report_sent = True
return 1
