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)