def main(argv):
'''PePr main function. Including preprocing and peak calling.
No post-processing'''
opt = optParser.opt_parser(argv)
parameter = optParser.process_opt(opt)
# read data and estimate the shiftsize, normalization constant
initialize.preprocess(parameter)
parameter.write_parameter_to_file()
# read data again, begin to process.
prepareData.read_files_to_arrays(parameter)
read_dict = prepareData.prepare_data(parameter)
if parameter.difftest is False:
swap = False
peakfilename = parameter.output_directory + parameter.name + "__PePr_peaks.bed"
sigTests.negative_binomial(read_dict, peakfilename, swap, parameter)
else:
up_peakfilename = parameter.output_directory + parameter.name + "__PePr_chip1_peaks.bed"
swap = False
sigTests.negative_binomial(read_dict, up_peakfilename, swap, parameter)
down_peakfilename = parameter.output_directory + parameter.name + "__PePr_chip2_peaks.bed"
swap = True
sigTests.negative_binomial(read_dict, down_peakfilename, swap,
parameter)
info("PePr finished running, thanks for all the wait!")
def main(argv):
## performing the option parser
opt = optParser.opt_parser(argv)
parameter, readData = optParser.process_opt(opt)
## read in the data
fileParser.parse(readData, parameter.file_format)
## remove the redundant reads
if (parameter.remove_redundant):
readData.remove_redundant_reads()
## shiftSize estimation and shifting reads
shiftSize.estimate_shift_size(readData,parameter)
shiftSize.shift_reads(readData)
file_in = open(argv[1], 'r')
file_passed = open(argv[1]+'_passed', 'w')
file_filtered = open(argv[1]+'_filtered', 'w')
post_processing(readData,file_in,file_passed,file_filtered)
def main(argv):
# initialize the logger
root_logger = logging.getLogger("")
debug = root_logger.debug
info = root_logger.info
# performing the option parser
opt = optParser.opt_parser(argv)
parameter, readData = optParser.process_opt(opt)
# 1. read and parse the data
fileParser.parse(readData, parameter.file_format)
# 2. remove the redundant reads
if (parameter.remove_redundant):
readData.remove_redundant_reads()
# 3. shiftSize estimation and shifting reads
shiftSize.estimate_shift_size(readData, parameter)
shiftSize.shift_reads(readData)
# 4. calculating the normalization constant
windowSize.estimate_normalization_constant(readData, parameter)
# 5. windowSize estimation and split reads into windows
windowSize.estimate_window_size(readData, parameter)
info (" The windowSize is %s", parameter.window_size)
windowSize.separate_exact_by_window(readData, parameter)
# 6. calling peaks
if parameter.difftest is False:
swap = False
peakfilename = parameter.name+"__PePr_peaks.bed"
sigTests.negative_binomial(readData, peakfilename, swap, parameter)
else:
up_peakfilename = parameter.name+"__PePr_up_peaks.bed"
swap = False
sigTests.negative_binomial(readData, up_peakfilename, swap, parameter)
down_peakfilename = parameter.name+"__PePr_down_peaks.bed"
swap = True
sigTests.negative_binomial(readData, down_peakfilename,
swap, parameter)
# 7. Write to a file that record the command and parameters.
parameter.write_parameter_to_file()
def main(argv):
# initialize the logger
root_logger = logging.getLogger("")
debug = root_logger.debug
info = root_logger.info
# performing the option parser
opt = optParser.opt_parser(argv)
parameter, readData = optParser.process_opt(opt)
# 1. read and parse the data
fileParser.parse(readData, parameter.file_format)
# 2. remove the redundant reads
if (parameter.remove_redundant):
readData.remove_redundant_reads()
# 3. shiftSize estimation and shifting reads
shiftSize.estimate_shift_size(readData, parameter)
shiftSize.shift_reads(readData)
# 4. calculating the normalization constant
windowSize.estimate_normalization_constant(readData, parameter)
# 5. windowSize estimation and split reads into windows
windowSize.estimate_window_size(readData, parameter)
info(" The windowSize is %s", parameter.window_size)
windowSize.separate_exact_by_window(readData, parameter)
# 6. calling peaks
if parameter.difftest is False:
swap = False
peakfilename = parameter.name + "__PePr_peaks.bed"
sigTests.negative_binomial(readData, peakfilename, swap, parameter)
else:
up_peakfilename = parameter.name + "__PePr_up_peaks.bed"
swap = False
sigTests.negative_binomial(readData, up_peakfilename, swap, parameter)
down_peakfilename = parameter.name + "__PePr_down_peaks.bed"
swap = True
sigTests.negative_binomial(readData, down_peakfilename, swap,
parameter)
# 7. Write to a file that record the command and parameters.
parameter.write_parameter_to_file()
def pre_processing_module():
opt = optParser.opt_parser(sys.argv)
parameter = optParser.process_opt(opt)
# read data and estimate the shiftsize, normalization constant
initialize.preprocess(parameter)
parameter.write_parameter_to_file()