# need to be set later 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
biochem.fill_with_air_to_valve(valve) elif method == 'flush_flowcell': print "INFO\t---\t-\t--> Please, enter name of reagent (Wash 1 / dH2O) to use as flush [string]: ", reagent = str(sys.stdin.readline().strip()) # use stdin explicitly and remove trailing newline character if reagent == 'Wash 1': port = 2 elif reagent == 'dH2O': port = 8 biochem.flush_flowcell(port) elif method == 'hyb': print "INFO\t---\t-\t--> Please, enter cycle name [string]: ", biochem.cycle = str(sys.stdin.readline().strip())[0:3] # use stdin explicitly and remove trailing newline character biochem.hyb() elif method == 'incubate_reagent': print "INFO\t---\t-\t--> Please, enter incubation time in minutes [integer]: ", time = int(sys.stdin.readline().strip()) # use stdin explicitly and remove trailing newline character biochem.incubate_reagent(time) elif method == 'init': biochem.init() elif method == 'lig_stepup_peg': print "INFO\t---\t-\t--> Please, enter cycle name [string]: ", biochem.cycle = str(sys.stdin.readline().strip())[0:3] # use stdin explicitly and remove trailing newline character biochem.lig_stepup_peg()