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)
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.
