def rep_case_control(rep_opt,logger=None): """Given the gridding scheme options, create simuPOP files in the given subdirectories.""" simuOpt.setOptions(alleleType='binary', optimized=True) from simuPOP import * cc_opt = simuOpt.Params(singleGeneModel.options) for maf in xrange(len(rep_opt.MAFs)): for maf_rep in xrange(rep_opt.MAF_replicates): maf_dir = "MAF_%.2f_%d" %(rep_opt.MAFs[maf],maf_rep+1) cc_opt.expandPop = "%s/%s.pop" % (maf_dir,maf_dir) cc_opt.pop = loadPopulation(cc_opt.expandPop) logger.info("Expanded population %s loaded!" %cc_opt.expandPop) for cc in xrange(len(rep_opt.CCs)): for cc_rep in xrange(rep_opt.CC_replicates): cc_dir = "cc_%d_%d" % (rep_opt.CCs[cc],cc_rep+1) for wtr in xrange(len(rep_opt.WTRs)): for wtr_rep in xrange(rep_opt.WTR_replicates): wtr_dir = "WTR_%.2f_%d" % (rep_opt.WTRs[wtr],wtr_rep+1) for grr in xrange(len(rep_opt.GRRs)): for grr_rep in xrange(rep_opt.GRR_replicates): grr_dir = "GRR_%.2f_%d" % (rep_opt.GRRs[grr],grr_rep+1) dirpath = path_maker(maf_dir,cc_dir,wtr_dir,grr_dir) cc_opt.wtr = rep_opt.WTRs[wtr] cc_opt.GRR = rep_opt.GRRs[grr] cc_opt.numControls= rep_opt.CCs[cc] cc_opt.sampledPop = os.path.join(dirpath,"sample.pop") pop = singleGeneModel.penetrance(cc_opt,logger) case_control_dataset.save(pars.sampledPop) logger.info("Sampled population saved at %s" %pars.sampledPop)
def single_mode(pipeline_pars,logger=None): if pipeline_pars.download: download_pars=downloadData(logger) if pipeline_pars.init: init_pop_pars =getInitPop(logger) if pipeline_pars.expand: expand_pop_pars = getExpandPop(logger) if pipeline_pars.penetrance: case_control_pars = getCaseControl(logger) if pipeline_pars.expand: if expand_pop_pars.filename == case_control_pars.expandPop: case_control_pars.pop = expand_pop_pars.expandPop logger.info("Using expandPop from simuGWAS!") else: case_control_pars.pop = simuPOP.loadPopulation(case_control_pars.expandPop) logger.info("Expanded population %s loaded!" %case_control_pars.expandPop) if os.path.isfile(case_control_pars.sampledPop): logger.info("Skipping case control dataset, file %s exists." %case_control_pars.sampledPop) else: case_control_dataset = singleGeneModel.penetrance(case_control_pars,logger) case_control_dataset.save(case_control_pars.sampledPop) logger.info("Sampled population saved at %s" %case_control_pars.sampledPop) if pipeline_pars.format: format_filenames = get_formatters(logger) if pipeline_pars.cline: cline_filenames = get_cline(logger)