else:
import ConfigParser # Import configuration parser class.
from logger import Logger # Import logger class.
from biochem import Biochem # Import biochecmistry class.
#--------------------- G.007 fluidics sub-system initialization ------------------------
config = ConfigParser.ConfigParser()
config.readfp(open('config.txt'))
t0 = time.time() # get current time
logger = Logger(config) # initialize logger object
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()
else:
import ConfigParser # Import configuration parser class.
from logger import Logger # Import logger class.
from biochem import Biochem # Import biochecmistry class.
#--------------------- Walkameter fluidics sub-system initialization -------------------
config = ConfigParser.ConfigParser()
config.readfp(open('config.txt'))
t0 = time.time() # get current time
print '\n'
logger = Logger(config) # initialize logger object
biochem = Biochem(logger) # Initialize biochemistry object: cycle-number need to be passed.
#---------------------------------------------------------------------------------------
# FLUIDICS SUB-SYSTEM FUNCTIONS
#---------------------------------------------------------------------------------------
logger.info('*\t--> Started %s method execution - biochem_utils.py' % sys.argv[1])
method = (sys.argv[1]) # assign name of requested method
if method == 'capping_1':
biochem.capping_1()
elif method == 'capping_2':
biochem.capping_2()
For: G.007 polony sequencer design [fluidics software] at the Church Lab -
Genetics Department, Harvard Medical School.
Purpose: polony_sequencing.py performs a polony sequencing biochemistry
consisting of given number of cycles of iteration (26)
This software may be used, modified, and distributed freely, but this
header may not be modified and must appear at the top of this file.
-------------------------------------------------------------------------------
"""
import sys
from biochem import Biochem # Import biochecmistry class.
#--------------------------- Configuration input handling ------------------------------
if len(sys.argv) < 3:
print '\n--> Error: not correct input!\n--> Usage: python polony_sequencing.py cycle-name flowcell-number\n'
sys.exit()
#--------------------- G.007 fluidics sub-system initialization ------------------------
t0 = time.time() # Get current time.
biochem = Biochem(
sys.argv[1], int(sys.argv[2])
) # Initialize biochemistry object - cycle-name and flowcell-number need to be passed.
#-------------------------- Alternating cycle iterations -------------------------------
biochem.run() # Run polony sequencing cycle(s).
#!/usr/local/bin/python
import sys
import time
import ConfigParser
from logger import Logger
from biochem import Biochem
config = ConfigParser.ConfigParser()
config.readfp(open('config.txt'))
t0 = time.time()
logger = Logger(config)
b = Biochem('WL1', 0, logger)
#b.mux.discrete_valve4_open()
b.mux.discrete_valve4_close()
import commands
import ConfigParser
from logger import Logger
from biochem import Biochem
print '\nINFO\t *\t--> START PRIMER WALKING MAIN - walking_main.py\n'
t0 = time.time() # get current time
config = ConfigParser.ConfigParser()
config.readfp(open('config.txt'))
cycle_iter = eval(config.get("cycle_constants", "cycle_iter"))
logger = Logger(config) # initialize logger object
biochem = Biochem(logger) # initialize biochemistry object
if biochem.speech_option == 1:
commands.getstatusoutput('mplayer -ao pulse ../../../speech/welcome.wav')
commands.getstatusoutput('mplayer -ao pulse ../../../speech/start.wav')
logger.info("*\t--> Started primer walking")
while (biochem.cycle < cycle_iter):
biochem.cycle += 1
if biochem.speech_option == 1:
commands.getstatusoutput('mplayer -ao pulse ../../../speech/cycle_' +
str(biochem.cycle) + '.wav')
biochem.run()
cycle_number_bio = 0
flowcell = 0
cycle_number_im = 0
if (installed_flowcells == 1):
for cycle_number in range(0, cycle_list_length):
cycle_list[cycle_number] = cycle_list[cycle_number].strip()
logger.info("---\t-\t--> Cycle_list key: %s" %
cycle_list[cycle_number])
logger.info("---\t-\t--> Cycle number: %i" % cycle_number)
cycle_list2 = cycle_list
if (cycle_list[cycle_number] == 'AM1g'):
time.sleep(0.1)
else:
biochem = Biochem(cycle_list[cycle_number], flowcell,
logger)
biochem.start()
while (biochem.isAlive()):
session.parse_read_string('y.ob[2]=1', '>')
session.parse_read_string('y.ob[2]=0', '>')
time.sleep(0.1)
# if(cycle_list[cycle_number] == 'WL1'):
# time.sleep(0.1)
# else:
# imager = PolonatorImager.Imager(cycle_list[cycle_number], flowcell)
# imager.start()
#
# while(imager.isAlive()):
# session.parse_read_string('y.ob[1]=1', '>')