# 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()
