biochem = Biochem('WL1', int(sys.argv[1]), logger) # Initialize biochemistry object - cycle-name and flowcell-number need to be passed. #--------------------------------------------------------------------------------------- # FLUIDICS SUB-SYSTEM FUNCTIONS #--------------------------------------------------------------------------------------- logger.info('***\t*\t--> Started %s method execution - fluidics_utils.py' % sys.arg[2]) if method is 'clean_V1_to_syringe': biochem.clean_V1_to_syringe() elif method is 'clean_V2_to_syringe': biochem.clean_V2_to_syringe() elif method is 'clean_flowcell_and_syringe': biochem.clean_flowcell_and_syringe() elif method is 'cycle_ligation': biochem.cycle_ligation() elif method is 'draw_air_to_mixer': print "\n***\t*\t--> Please, enter air gap size [integer]: ", gap_size = int(sys.stdin.readline().strip()) # use stdin explicitly and remove trailing new-line character biochem.draw_air_to_mixer(gap_size) elif method is 'draw_air_to_syringe': biochem.draw_air_to_syringe() elif method is 'draw_air_to_valve': print "\n***\t*\t--> Please, enter valve name air to be drawn (V1, V2, V3, V5) [string]: ", valve = str(sys.stdin.readline().strip()) # use stdin explicitly and remove trailing new-line character
#--------------------------------------------------------------------------------------- # FLUIDICS SUB-SYSTEM FUNCTIONS #--------------------------------------------------------------------------------------- logger.info('***\t*\t--> Started %s method execution - fluidics_utils.py' % sys.arg[2]) if method is 'clean_V1_to_syringe': biochem.clean_V1_to_syringe() elif method is 'clean_V2_to_syringe': biochem.clean_V2_to_syringe() elif method is 'clean_flowcell_and_syringe': biochem.clean_flowcell_and_syringe() elif method is 'cycle_ligation': biochem.cycle_ligation() elif method is 'draw_air_to_mixer': print "\n***\t*\t--> Please, enter air gap size [integer]: ", gap_size = int(sys.stdin.readline().strip( )) # use stdin explicitly and remove trailing new-line character biochem.draw_air_to_mixer(gap_size) elif method is 'draw_air_to_syringe': biochem.draw_air_to_syringe() elif method is 'draw_air_to_valve': print "\n***\t*\t--> Please, enter valve name air to be drawn (V1, V2, V3, V5) [string]: ",
if method == 'capping_1': biochem.capping_1() elif method == 'capping_2': biochem.capping_2() elif method == 'clean_flowcell': print "INFO\t *\t--> Please, enter reagent and cleaning iteration numbers separated by single space [integers]: ", v = sys.stdin.readline().strip().split(' ') # use stdin explicitly and remove trailing newline character biochem.clean_flowcell(int(v[0]), int(v[1])) elif method == 'clean_flowcell_and_syringe': print "INFO\t *\t--> Please, enter the number of cleaning iterations [integer]: ", iteration = int(sys.stdin.readline().strip()) # use stdin explicitly and remove trailing newline character biochem.clean_flowcell_and_syringe(iteration) elif method == 'clean_fluidics_system': print "INFO\t *\t--> Please, enter the number of cleaning iterations [integer]: ", iteration = int(sys.stdin.readline().strip()) # use stdin explicitly and remove trailing newline character biochem.clean_fluidics_system(iteration) elif method == 'clean_reagent_path': print "INFO\t *\t--> Please, enter: reagent and iteration numbers separated by single space [integers]: ", v = sys.stdin.readline().strip().split(' ') # use stdin explicitly and remove trailing newline character biochem.clean_reagent_path(int(v[0]), int(v[1])) elif method == 'clean_syringe_pump': print "INFO\t *\t--> Please, enter the number of cleaning iterations [integer]: ", iteration = int(sys.stdin.readline().strip()) # use stdin explicitly and remove trailing newline character biochem.clean_syringe_pump(iteration)