if reagent is 'Wash 1': port = 2 else: port = 8 biochem.flush_flowcell(port) elif method is 'hyb': biochem.hyb() elif method is 'incubate_reagent': print "\n***\t*\t--> Please, enter minutes for incubation [integer]: ", time = int(sys.stdin.readline().strip( )) # use stdin explicitly and remove trailing new-line character biochem.incubate_reagent(time) elif method is 'init': biochem.init() else: print '\n***\t*\t--> Error: not correct method input!\n--> Double check method name (2nd argument)\n' sys.exit() #-------------------------- Duration of biochemistry test ------------------------------ delta = (time.time() - t0) / 60 # Calculate elapsed time for flowcell flush. logger.warn( '***\t*\t--> Finished %s method execution - duration: %0.2f minutes\n\n' % delta)
logger.info('***\t*\t--> Started biochemistry object testing - biochem_test.py') #--------------------------------- Initialization -------------------------------------- #biochem.syringe_pump_init() #biochem.reagent_block_init() # Set reagent block cooler to constant temperature, 4 Celsius degrees. #biochem.rotary_valve1_init() # Initialize reagent start points in ten port rotary valve V1. #biochem.rotary_valve2_init() # Initialize reagent start points in ten port rotary valve V2. #biochem.rotary_valve3_init() # Initialize reagent start points in ten port rotary valve V3. #biochem.syringe_pump_init() # Initializes syringe pump by moving it to zero position and setting speed to 20. #biochem.mixer_init() # Prime mixer chamber with Wash 1 as initialization step. #biochem.ligase_init() # Initialize ligase/ligase buffer start points in nine port valve V0. biochem.init() # Initialize biochemistry sub-system. #------------------------------- Complex functions ------------------------------------- #biochem.get_config_parameters() # Retieves all biochemistry and device related configuration parameters configuration file. #biochem.get_excel_volumes() # Extracts path length and tube cross-sectional area information from standard Excel file. #biochem.clean_V1_to_syringe() # Fills tube path V1 to syringe port 5 with Wash 1 and dumps previous tube content to waste. #biochem.clean_V2_to_syringe() # Fills tube path V2 to syringe port 6 with Wash 1 and dumps previous tube content to waste. #biochem.draw_air_to_syringe() # Draws a specific volume of air plug to syringe's COM-port. #biochem.draw_air_to_valve('V3') # Draws a specific volume of air plug to specified valve COM-port. #biochem.move_reagent(1000, 20, 4, 30, 7) # Moves a given volume of reagent from one syringe port to another at different speeds. #biochem.draw_into_flowcell(1000) # Draws reagent into flowcell. #biochem.flush_flowcell(5) # Flushes flowcell 3-times with Wash 1 or dH20.
port = 2 else: port = 8 biochem.flush_flowcell(port) elif method is 'hyb': biochem.hyb() elif method is 'incubate_reagent': print "\n***\t*\t--> Please, enter minutes for incubation [integer]: ", time = int(sys.stdin.readline().strip()) # use stdin explicitly and remove trailing new-line character biochem.incubate_reagent(time) elif method is 'init': biochem.init() else: print '\n***\t*\t--> Error: not correct method input!\n--> Double check method name (2nd argument)\n' sys.exit() #-------------------------- Duration of biochemistry test ------------------------------ delta = (time.time() - t0) / 60 # Calculate elapsed time for flowcell flush. logger.warn('***\t*\t--> Finished %s method execution - duration: %0.2f minutes\n\n' % delta)