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':
reagent = "Wash 1"
biochem.draw_into_flowcell(9, sys.argv[3], int(sys.argv[4]), \
int(sys.argv[5]))
# usage: biochem_utils.py fcnum draw_into_flowcell_bufferchase
elif method == 'draw_into_flowcell_bufferchase':
reagent = "Wash 1"
biochem.draw_into_flowcell_bufferchase(9, sys.argv[3], \
int(sys.argv[4]), int(sys.argv[5]), int(sys.argv[6]), \
int(sys.argv[7]) )
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.fill_with_air_to_valve(valve)
elif method is 'flush_flowcell':
print "\n***\t*\t--> Please, enter reagent to use (Wash 1 / dH2O) [string]: ",
reagent = str(sys.stdin.readline().strip(
)) # use stdin explicitly and remove trailing new-line character
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'
elif method is 'fill_with_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.fill_with_air_to_valve(valve)
elif method is 'flush_flowcell':
print "\n***\t*\t--> Please, enter reagent to use (Wash 1 / dH2O) [string]: ",
reagent = str(sys.stdin.readline().strip()) # use stdin explicitly and remove trailing new-line character
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()
