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Commit 879f06d4 authored by Todor Kondic's avatar Todor Kondic
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Fix idir

* R/mix.r(p.sw,v): idir
parent e8540eac
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...@@ -219,7 +219,7 @@ mb.single<-function(mb,infodir,fn_stgs) { ...@@ -219,7 +219,7 @@ mb.single<-function(mb,infodir,fn_stgs) {
##' from data filenames. ##' from data filenames.
##' @author Todor Kondić ##' @author Todor Kondić
v<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="archive",lastStep=8,combine=F) { v<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="archive",lastStep=8,combine=F) {
idir<-function(n) file.path(rdir,stripext(n)) idir<-function(n) file.path(".",stripext(n))
f<-Vectorize(single.sw,vectorize.args=c("wd","fn_data","stgs_alist"),SIMPLIFY=F) f<-Vectorize(single.sw,vectorize.args=c("wd","fn_data","stgs_alist"),SIMPLIFY=F)
rootdir <- getwd() rootdir <- getwd()
if (combine) { if (combine) {
...@@ -267,6 +267,7 @@ v<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="ar ...@@ -267,6 +267,7 @@ v<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="ar
##' from data filenames. ##' from data filenames.
##' @author Todor Kondić ##' @author Todor Kondić
p.sw<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="archive",lastStep=8,combine=F,cl=NULL) { p.sw<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="archive",lastStep=8,combine=F,cl=NULL) {
idir<-function(n) file.path(".",stripext(n))
fnocomb<-function(fn,stgs,wd) { fnocomb<-function(fn,stgs,wd) {
single.sw(fn,stgs,wd,fn_cmpd_list,mode,readMethod,archdir,lastStep=lastStep) single.sw(fn,stgs,wd,fn_cmpd_list,mode,readMethod,archdir,lastStep=lastStep)
} }
...@@ -279,12 +280,17 @@ p.sw<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir= ...@@ -279,12 +280,17 @@ p.sw<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir=
z<-parallel::clusterMap(cl,fcomb,fn_data,stgs_alist,wd) z<-parallel::clusterMap(cl,fcomb,fn_data,stgs_alist,wd)
names(z)<-basename(fn_data) names(z)<-basename(fn_data)
zz<-RMassBank::combineMultiplicities(z) zz<-RMassBank::combineMultiplicities(z)
combdir<-"combined" combdir<-"combined"
archdir<-file.path(rootdir,combdir,archdir) archdir<-file.path(rootdir,combdir,archdir)
no_drama_mkdir(combdir) no_drama_mkdir(combdir)
no_drama_mkdir(archdir) no_drama_mkdir(archdir)
fn_arch<-file.path(archdir,"archive") fn_arch<-file.path(archdir,"archive")
fn_comb_stgs <- file.path(rootdir,combdir,paste(combdir,".mzML.ini",sep=''))
ddirs <- sapply(names(z),idir)
stgs_fls <- sapply(ddirs,function(x) file.path(x,paste(x,".mzML.ini",sep='')))
mk_combine_file(stgs_fls,fn_comb_stgs)
res<-list(RMassBank::msmsWorkflow(zz, steps=8, mode=mode, archivename = fn_arch)) res<-list(RMassBank::msmsWorkflow(zz, steps=8, mode=mode, archivename = fn_arch))
names(res)<-paste(combdir,".yml",sep='') #Clearly a hack. names(res)<-paste(combdir,".yml",sep='') #Clearly a hack.
res res
......
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