Remove mix.R

mix.R

-## Create a temporary directory to hold the files generated on the
-## fly.
-rmbmix.mkdir<-function() {
-    nm<-tempfile(pattern="rmbmix")
-    dir.create(nm)
-    nm
-}
-
-##
-rmbmix.mk_sett_file<-function(sett_alist,file) {
-    require(yaml)
-    tmp<-tempfile()
-    RmbSettingsTemplate(tmp)
-    sett<-yaml.load_file(tmp)
-    for (nm in names(sett_alist)) {
-        sett[[nm]]<-sett_alist[[nm]]
-    }
-    write_yaml(x=sett,file=file)
-}
-
-
-## Generate the RMassBank compound list from the input compound list
-## in CSV file src_fn. The input compound list format is either
-## Chemical Dashboard csv file with, at least, PREFERRED_NAMES and
-## SMILES columns _filled_ out, or just an ordinary csv file with
-## columns SMILES and Names filled. Argument dest_fn is the
-## destination filename. Returns the number of compounds.
-rmbmix.gen_comp_list<-function(src_fn,dest_fn) {
-    df<-read.csv(src_fn)
-    ## Names
-    nms<-if ("PREFERRED_NAME" %in% names(df)) df$PREFERRED_NAME else df$Name
-    if (is.null(nms)) stop("Unable to read compound names from the input compound list.")
-
-    ## SMILES
-    haha<-df$SMILES
-    sz<-length(haha)
-    
-    ## CAS
-    casvals<-if ("CASRN" %in% names(df)) df$CASRN else rep(NA,sz)
-    if (is.null(haha)) stop("Unable to read SMILES from the input compound list.")
-
-    outdf<-data.frame(ID=1:sz,Name=nms,SMILES=haha,CAS=casvals,RT=rep(NA,sz))
-    write.csv(outdf,file=dest_fn,row.names=F,na="")
-    length(nms)
-}
-    
-    
-    
-## Perform the compound mixture workflow on the data file called
-## fn_data with settings named list called stgs_alist. Alternatively,
-## stg_alist can be a file name which follows the RMassBank settings
-## specification, also in YAML format, containing only parts that
-## differ from the default. Argument fn_cmpd_list is the compound
-## list. Argument wd is the scratch dir to hold generated ini files
-## and the like. Arguments mode and readMethod are the same as in
-## msmsRead.
-rmbmix.single<-function(fn_data,stgs_alist,fn_cmpd_list,wd,mode,readMethod="mzR",archdir="archive") {
-    
-    require(RMassBank)
-    require(yaml)
-    ## Generate settings file and load.
-    stgs_alist<-if (is.character(stgs_alist)) yaml.load_file(stgs_alist) else stgs_alist
-    sfn<-file.path(wd,paste(fn_data,".ini",sep=''))
-    rmbmix.mk_sett_file(stgs_alist,sfn)
-    loadRmbSettings(sfn)
-
-    ## Generate and load the compound list.
-    fn_comp<-file.path(wd,paste(fn_data,".comp.csv",sep=''))
-    n_cmpd<-rmbmix.gen_comp_list(fn_cmpd_list,fn_comp)
-    loadList(fn_comp)
-
-    ## Generate file table.
-    df_table<-data.frame(Files=rep(fn_data,n_cmpd),ID=1:n_cmpd)
-    fn_table<-file.path(wd,paste("fn-table.",fn_data,".csv",sep=''))
-    write.csv(x=df_table,file=fn_table,row.names=F)
-
-    ## Make empty workspace.
-    w <- newMsmsWorkspace()
-    ## Run the workflow.
-    message(paste("Reading in file:",fn_data))
-    w <-msmsRead(w,filetable=fn_table,readMethod="mzR",mode=mode)
-    if (!dir.exists(archdir)) dir.create(archdir)
-    fn_arch<-file.path(archdir,paste(fn_data,".archive",sep=''))
-    w<-msmsWorkflow(w, mode=mode, steps=2:8,archivename=fn_arch)
-    mb<-newMbWorkspace(w)
-    mb<-resetInfolists(mb)
-    ## loadInfolists
-    ## addPeaks
-    bits<-strsplit(fn_data,split="\\.")[[1]]
-    fn_info<-if (length(bits)> 1) paste(head(bits,-1),collapse=".") else fn_data
-    infodir<-fn_info
-    fn_info<-paste(archdir,"/",fn_info,".csv",sep='')
-    mb<-mbWorkflow(mb,infolist_path=fn_info)
-    list(w=w,mb=mb)
-}
-
-
-rmbmix.mb2.single<-function(mb,infodir) {
-    mb <- resetInfolists(mb)
-    mb <- loadInfolists(mb,infodir)
-    mbWorkflow(mb)
-}
-rmbmix.mb2<-Vectorize(rmbmix.mb2.single,vectorize.args=c("mb","infodir"),SIMPLIFY=F)
-rmbmix<- Vectorize(rmbmix.single,vectorize.args=c("fn_data","stgs_alist"),SIMPLIFY=F)