bin/subSampleTumorTypes.R

In Sage-Bionetworks/dten: Infers drugs of interest based on expression

require(optparse)




getArgs<-function(){

    option_list<-list(
        make_option(c('-f','--folderid'),dest='folder',help='Synapse id of folder containing files'),
        make_option(c('-n','--number'),dest='num',help='Number to sample',default=10),
        make_option(c('-v','--fileview'),dest='fv',help='Fileview to query'))

    args=parse_args(OptionParser(option_list = option_list))
    return(args)
}

main<-function(){
    args<-getArgs()
    require(synapser)
    synLogin(silent=TRUE)

    invisible(capture.output(res<-sample(x=synapser::synTableQuery(paste0('select id from ',args$fv,' where parentId = \'',args$folder,'\''))$asDataFrame()$id,args$num)))
    cat(res,sep='\n')
}

main()