#--------------------------------------------------------------------------------------- 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 biochem.draw_air_to_valve(valve)
biochem = Biochem('WL1', int(sys.argv[1])) method = sys.argv[2] log.info("---\t-\t--> Started %s method execution - biochem_utils.py" % \ (method)) # usage: biochem_utils.py fcnum cycle_ligation cyclename # cyclename must be a valid cyclename that has a nonamer/hyb # valve/port mapping in sequencing.cfg # cyclename can be either 3 or 4 chars in length if method == 'cycle_ligation': biochem.flowcell = int(sys.argv[1]) biochem.cycle_name = sys.argv[3] biochem.cycle = biochem.cycle_name[0:3] biochem.cycle_ligation() # usage: biochem_utils.py fcnum flush_flowcell elif method == 'flush_flowcell': reagent = "Wash 1" if reagent == 'Wash 1': port = 9 elif reagent == 'dH2O': port = 7 biochem.flush_flowcell(9) #biochem.rinse(int(sys.argv[1])) # usage: biochem_utils.py fcnum draw_into_flowcell elif method == 'draw_into_flowcell':