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#!/usr/bin/python3
__doc__="""
pliu 20150510
run pRSEM to calculate priors and use them for abundance estimation
"""
import os
import sys
import Util
import Prsem
def main():
import Param
argdict = getCommandLineArguments()
param = Param.initFromCommandLineArguments(argdict)
if param.chipseq_peak_file is None:
if param.partition_model == 'cmb_lgt':
if param.chipseq_bed_files_multi_targets is not None:
Prsem.genChIPSeqSignalFilesFromBed(param)
elif param.chipseq_read_files_multi_targets is not None:
Prsem.genChIPSeqSignalFilesFromReads(param)
else:
## IDR peaks will be saved in file param.fidr_chipseq_peaks
Prsem.genChIPSeqPeakFileBySPPIDR(param)
if param.partition_model == 'pk':
## no need to calculate signals or body/tes peaks here
Prsem.genPriorByTSSPeak(param)
elif param.partition_model == 'cmb_lgt':
Prsem.genPriorByCombinedTSSSignals(param)
else:
genPriorByPeakSignalGCLen(param)
Prsem.runGibbsSampling(param)
def getCommandLineArguments():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--num-threads', type=int)
parser.add_argument('--chipseq-target-read-files')
parser.add_argument('--chipseq-control-read-files')
parser.add_argument('--chipseq-read-files-multi-targets')
parser.add_argument('--chipseq-bed-files-multi-targets')
parser.add_argument('--cap-stacked-chipseq-reads', action='store_true')
parser.add_argument('--n-max-stacked-chipseq-reads', type=int)
parser.add_argument('--bowtie-path')
parser.add_argument('--chipseq-peak-file')
parser.add_argument('--partition-model', )
parser.add_argument('--gibbs-burnin', type=int)
parser.add_argument('--gibbs-number-of-samples', type=int)
parser.add_argument('--gibbs-sampling-gap', type=int)
parser.add_argument('--quiet', action='store_true')
## need to be in the same order as fed in argument
parser.add_argument('ref_name')
parser.add_argument('sample_name')
parser.add_argument('stat_name')
parser.add_argument('imd_name')
argdict = vars(parser.parse_args())
return argdict
if __name__=='__main__':
main()
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