#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()