#biochem.draw_air_to_syringe() # Draws a specific volume of air plug to syringe's COM-port.
#biochem.draw_air_to_valve('V3') # Draws a specific volume of air plug to specified valve COM-port.
#biochem.move_reagent(1000, 20, 4, 30, 7) # Moves a given volume of reagent from one syringe port to another at different speeds.
#biochem.draw_into_flowcell(1000) # Draws reagent into flowcell.
#biochem.flush_flowcell(5) # Flushes flowcell 3-times with Wash 1 or dH20.
#biochem.prime_flowcells() # Prime both flowcells with Wash 1 as initialization step.
#biochem.set_to_RT() # Sets temperataure controller to room temperature (28 C).
#biochem.incubate_reagent(1) # Incubates reagent for given amount of time.
#biochem.wait_for_SS(15) # Waits until steady-state temperature is reached, or exits wait block if ramping.
#biochem.nonamer_prep('V1', 1) # Moves nonamer and ligase into mixing chamber.
#biochem.ligase_mix(10) # Mixes ligase with nonamer in mixing chamber.
"""
biochem.move_reagent(biochem.mixer_to_V5, biochem.pull_speed, 2, biochem.empty_speed, 4) # draw "Wash 1" from mixer through flowcell to waste
biochem.move_reagent(biochem.syringe_1_to_mixer, biochem.pull_speed, 1, biochem.pull_speed, 4) # clear path syringe port 1 to mixing chamber inlet 1
biochem.move_reagent(biochem.syringe_8_to_mixer, biochem.pull_speed, 8, biochem.pull_speed, 4) # clear path syringe port 8 to mixing chamber inlet 2
"""
#---------------------------- Biochemistry functions -----------------------------------
#biochem.exo_start() # Performs biochemistry to prepare polony sequencing run.
#biochem.enzyme_reaction() # Digests unprotected bead-bound ePCR primers with Exonuclease I using rotary valve 2.
#biochem.strip_chem() # Performs chemical stripping protocol for polony sequencing.
#biochem.hyb(4) # Runs primer hybridization protocol for polony sequencing.
#biochem.lig_stepup_peg(4, 'V1', 1) # Runs stepup peg ligation reaction protocol for polony sequencing.
#biochem.cycle_ligation() # Performs a cycle of polony sequencing biochemistry.
elif method == 'incorporation':
biochem.incorporation()
elif method == 'incubate_reagent':
print "INFO\t *\t--> Please, enter incubation time in minutes [integer]: ",
time_m = int(sys.stdin.readline().strip()) # use stdin explicitly and remove trailing newline character
biochem.incubate_reagent(time_m)
elif method == 'init':
biochem.init()
elif method == 'move_reagent':
print "INFO\t *\t--> Please, enter: fill_volume, from_speed, from_port, to_speed, to_port separated by single space [integers]: ",
v = sys.stdin.readline().strip().split(' ') # use stdin explicitly and remove trailing newline character
biochem.move_reagent(int(v[0]), int(v[1]), int(v[2]), int(v[3]), int(v[4]))
elif method == 'move_reagent_slow':
print "INFO\t *\t--> Please, enter: fill_volume, from_speed, from_port, to_speed, to_port separated by single space [integers]: ",
v = sys.stdin.readline().strip().split(' ') # use stdin explicitly and remove trailing newline character
biochem.move_reagent_slow(int(v[0]), int(v[1]), int(v[2]), int(v[3]), int(v[4]))
elif method == 'pre_washing':
biochem.pre_washing()
elif method == 'prime_flowcell':
biochem.prime_flowcell()
elif method == 'prime_fluidics_system':
biochem.prime_fluidics_system()
#biochem.draw_air_to_syringe() # Draws a specific volume of air plug to syringe's COM-port.
#biochem.draw_air_to_valve('V3') # Draws a specific volume of air plug to specified valve COM-port.
#biochem.move_reagent(1000, 20, 4, 30, 7) # Moves a given volume of reagent from one syringe port to another at different speeds.
#biochem.draw_into_flowcell(1000) # Draws reagent into flowcell.
#biochem.flush_flowcell(5) # Flushes flowcell 3-times with Wash 1 or dH20.
#biochem.prime_flowcells() # Prime both flowcells with Wash 1 as initialization step.
#biochem.set_to_RT() # Sets temperataure controller to room temperature (28 C).
#biochem.incubate_reagent(1) # Incubates reagent for given amount of time.
#biochem.wait_for_SS(15) # Waits until steady-state temperature is reached, or exits wait block if ramping.
#biochem.nonamer_prep('V1', 1) # Moves nonamer and ligase into mixing chamber.
#biochem.ligase_mix(10) # Mixes ligase with nonamer in mixing chamber.
"""
biochem.move_reagent(biochem.mixer_to_V5, biochem.pull_speed, 2, biochem.empty_speed, 4) # draw "Wash 1" from mixer through flowcell to waste
biochem.move_reagent(biochem.syringe_1_to_mixer, biochem.pull_speed, 1, biochem.pull_speed, 4) # clear path syringe port 1 to mixing chamber inlet 1
biochem.move_reagent(biochem.syringe_8_to_mixer, biochem.pull_speed, 8, biochem.pull_speed, 4) # clear path syringe port 8 to mixing chamber inlet 2
"""
#---------------------------- Biochemistry functions -----------------------------------
#biochem.exo_start() # Performs biochemistry to prepare polony sequencing run.
#biochem.enzyme_reaction() # Digests unprotected bead-bound ePCR primers with Exonuclease I using rotary valve 2.
#biochem.strip_chem() # Performs chemical stripping protocol for polony sequencing.
#biochem.hyb(4) # Runs primer hybridization protocol for polony sequencing.
#biochem.lig_stepup_peg(4, 'V1', 1) # Runs stepup peg ligation reaction protocol for polony sequencing.
#biochem.cycle_ligation() # Performs a cycle of polony sequencing biochemistry.
