lower_limit = read_req - (read_req * 0.1)
print libid, read_req, lower_limit, readcount
self.show_log('info', "{0}.{1} - Library(ies) with read requested set to 0 - {2}".format(self.__classname, getframe().f_code.co_name, self.__zeroread))
self.show_log('info', "{0}.{1} - Library(ies) with no tracks - {2}".format(self.__classname, getframe().f_code.co_name, self.__zerotrack))
self.show_log('info', "{0}.{1} - Library(ies) with FQ-files not done - {2}".format(self.__classname, getframe().f_code.co_name, self.__zerofqfile))
'''
check library status for 'sequencing'
query reads requested for the libraries
if reads_requested - 10% is matched -> set libraries to finished/data delivered
if data_delivered -> publish reads
question: how find out if finished/data delivered -> via project? what if there are more than one project?
'''
if __name__ == '__main__':
db = Database(Information.DB_HOST, Information.DB_USER, Information.DB_PW, Information.DB)
logfile = '{0}{1}'.format(Information.LOGDIRECTORY, getLogfile(basename(getframe().f_code.co_filename.rstrip('.py'))))
mainlog = MainLogger(logfile)
db_main = DB_Maintain(db)
db_main.start_logging()
db.start_logging()
db.setConnection()
db_main.check_library_delivery_state()
#db_main.check_library_sequencing_amount()
db.commitConnection()
db.closeConnection()
self.register_fqfiles()
self.prepare_SGElist()
if self.__array:
self.build_ArrayJob()
self.writeArrayFiles()
self.writeSGE()
self.startSGE()
sgelist = property(get_sgelist)
if __name__ == '__main__':
db = None
parser = Parser()
parser.parse()
parser.start_logging()
if parser.log:
logfile = '{0}{1}'.format(Information.LOGDIRECTORY, getLogfile(basename(getframe().f_code.co_filename.rstrip('.py'))))
mainlog = MainLogger(logfile)
parser.main()
if parser.query:
db = Database(Information.DB_HOST, Information.DB_USER, Information.DB_PW, Information.DB)
if parser.log: db.start_logging()
db.setConnection()
trinst = TransportFastq(parser.log, parser.files, parser.output, parser.zip, parser.array, parser.merge, parser.undet, parser.query, db)
trinst.main()
if parser.query:
db.closeConnection()
