From b97e2d511ccf2228c423083cd5a095f391fd1d27 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Fri, 28 Jun 2019 02:05:31 +0200
Subject: [PATCH] Major reorg
---
R/mix.R | 387 +++++++++++++++++---------------------------------------
R/run.R | 80 ++++++++----
2 files changed, 173 insertions(+), 294 deletions(-)
diff --git a/R/mix.R b/R/mix.R
index 203667a..6edc37c 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -7,13 +7,14 @@ stripext<-function(fn) {
##' Create directories without drama.
##'
##' @title Create directories without drama
-##' @param path Name of the directory.
+##' @param path Names of the directories.
##' @return The character string containing the input argument `path`.
##' @author Todor Kondić
no_drama_mkdir<-function(path) {
-
- if (! dir.exists(path)) dir.create(path)
- path
+ f <- Vectorize(function(path) {
+ if (! dir.exists(path)) dir.create(path)
+ path},vectorize.args="path")
+ f(path)
}
##' Produce the Rmb Settings file
@@ -60,6 +61,59 @@ mk_combine_file<-function(sett_fns,fname) {
fname
}
+
+fn_data2wd <- function(fn_data,dest) {
+
+ f <- Vectorize(function(fn_data) {
+ noext <- stripext(fn_data)
+ file.path(dest,basename(noext))
+ },vectorize.args="fn_data")
+ f(fn_data)
+}
+
+
+
+get_cmpd_l_fn <- function(wd) {
+ f <- function(wd) file.path(wd,"compounds.csv")
+ fv <- Vectorize(f,vectorize.args=c("wd"))
+ fv(wd)
+}
+
+get_stgs_fn <- function(wd) {
+ f <- function(wd) file.path(wd,"settings.ini")
+ fv <- Vectorize(f,vectorize.args=c("wd"))
+ fv(wd)
+}
+
+get_ftable_fn <- function(wd) {
+ f <- function(wd) file.path(wd,"ftable.ini")
+ fv <- Vectorize(f,vectorize.args=c("wd"))
+ fv(wd)
+}
+
+get_inp_stgs_fn<- function(fn_data) {
+ f <- Vectorize(function(fn_data) {
+ bnm <- stripext(fn_data)
+ fn <- paste(bnm,".ini",sep='')},
+ vectorize.args="fn_data")
+ f(fn_data)}
+
+get_info_dir <- function(wd) {
+ file.path(wd,"info")
+}
+
+get_info_fn <- function(wd) {
+ file.path(get_info_dir(wd),"info.csv")
+}
+
+gen_info_dir <- function(wd) {
+ nm <- get_info_dir(wd)
+ no_drama_mkdir(nm)
+ nm
+}
+
+
+
##' Generate the RMassBank compound list from the input compound list
##' in CSV file src_fn. The input compound list format is either a
##' Chemical Dashboard csv file with, at least, PREFERRED_ SMILES
@@ -67,13 +121,12 @@ mk_combine_file<-function(sett_fns,fname) {
##' SMILES and Names filled. Argument dest_fn is the destination
##' filename. Returns the number of compounds.
##'
-##'
##' @title Generate Compound List File
##' @param src_fn The input compound list CSV filename.
##' @param dest_fn The resulting compound list CSV filename.
##' @return Number of compounds.
##' @author Todor Kondić
-gen_comp_list<-function(src_fn,dest_fn) {
+gen_cmpd_l<-function(src_fn,dest_fn) {
df<-read.csv(src_fn)
## Names
nms<-if ("PREFERRED_NAME" %in% names(df)) df$PREFERRED_NAME else df$Name
@@ -87,41 +140,40 @@ gen_comp_list<-function(src_fn,dest_fn) {
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="")
+ f <- Vectorize(function (dest_fn) {
+ write.csv(outdf,file=dest_fn,row.names=F,na="")
+ },vectorize.args="dest_fn",SIMPLIFY=F)
+
+ f(dest_fn)
length(nms)
}
##' Generates settings file and loads it.
##'
-##'
##' @title Generate and Load the RMassBank Settings File
-##' @param fn_data The mzML filename.
##' @param stgs Settings named list, or a settings filename.
##' @param wd Directory under which results are archived.
##' @return result of RMassBank::loadRmbSettings
##' @author Todor Kondić
-gen_stgs_and_load <- function(fn_data,stgs,wd) {
+gen_stgs_and_load <- function(stgs,wd) {
stgs<-if (is.character(stgs)) yaml::yaml.load_file(stgs) else stgs
- sfn<-file.path(wd,paste(basename(fn_data),".ini",sep=''))
+ sfn<-get_stgs_fn(wd)
mk_sett_file(stgs,sfn)
RMassBank::loadRmbSettings(sfn)
}
##' Generates the RMassBank compound list and loads it.
##'
-##'
##' @title Generate and Load the RMassBank Compound List
-##' @param fn_data The mzML filename.
##' @param wd Directory under which results are archived.
+##' @param fn_cmpdl The input compound list filename.
##' @return Named list. The key `fn_cmpdl` is the path of the
##' generated compound list and the key `n` the number of
##' compounds.
##' @author Todor Kondić
-gen_cmpdl_and_load <- function(fn_data,wd,fn_cmpdl) {
- wd <- normalizePath(wd)
- fn_data <- normalizePath(fn_data)
- fn_comp<-file.path(wd,paste(basename(fn_data),".comp.csv",sep=''))
- n_cmpd<-gen_comp_list(fn_cmpdl,fn_comp)
+gen_cmpdl_and_load <- function(wd,fn_cmpdl) {
+ fn_comp<-get_cmpd_l_fn(wd)
+ n_cmpd<-gen_cmpd_l(fn_cmpdl,fn_comp)
RMassBank::loadList(fn_comp)
list(fn_cmpdl=fn_comp,n=n_cmpd)
}
@@ -131,17 +183,50 @@ gen_cmpdl_and_load <- function(fn_data,wd,fn_cmpdl) {
##'
##' @title Generate and Load the RMassBank Settings File
##' @param fn_data The mzML filename.
-##' @param n_cmpd Number of compounds.
##' @param wd Directory under which results are archived.
+##' @param n_cmpd Number of compounds.
##' @return File path of the file table.
##' @author Todor Kondić
-gen_file_table <- function(fn_data,n_cmpd,wd) {
- wd <- normalizePath(wd)
- fn_data <- normalizePath(fn_data)
- df_table<-data.frame(Files=rep(fn_data,n_cmpd),ID=1:n_cmpd)
- fn_table<-file.path(wd,paste("fn-table.",basename(fn_data),".csv",sep=''))
- write.csv(x=df_table,file=fn_table,row.names=F)
- fn_table
+gen_ftable <- function(fn_data,wd,n_cmpd) {
+ f <- Vectorize(function(fn_data,wd) {
+ df_table<-data.frame(Files=rep(fn_data,n_cmpd),ID=1:n_cmpd)
+ fn_table<-get_ftable_fn(wd)
+ write.csv(x=df_table,file=fn_table,row.names=F)
+ fn_table
+ }, vectorize.args=c("fn_data","wd"))
+
+ f(fn_data,wd)
+}
+
+gen_fn_stgs <- function(fn_inp,fn) {
+ f <- Vectorize(function(fn_inp,fn) {
+ stgs <- yaml::yaml.load_file(fn_inp)
+ mk_sett_file(stgs,fn)
+ fn}, vectorize.args=c("fn_inp","fn"))
+
+ f(fn_inp,fn)
+}
+
+conf <- function(fn_data,fn_cmpd_l,dest) {
+ no_drama_mkdir(dest)
+ wd <- fn_data2wd(fn_data,dest)
+ no_drama_mkdir(wd)
+ fn_inp_stgs <- get_inp_stgs_fn(fn_data)
+ fn_stgs <- get_stgs_fn(wd)
+ fn_out_cmpd_l <- get_cmpd_l_fn(wd)
+
+ gen_fn_stgs(fn_inp_stgs,fn_stgs)
+ n_cmpd <- gen_cmpd_l(fn_cmpd_l,fn_out_cmpd_l)
+ gen_ftable(fn_data,wd,n_cmpd)
+}
+
+reconf <- function(wd) {## Load the settings.
+ fn_stgs <- get_stgs_fn(wd)
+ RMassBank::loadRmbSettings(fn_stgs)
+
+ ## Load the compound list.
+ fn_cmpd_l <- get_cmpd_l_fn(wd)
+ RMassBank::loadList(fn_cmpd_l)
}
##' Wrapper for a single prescreening call. Produces output in the
@@ -160,12 +245,11 @@ gen_file_table <- function(fn_data,n_cmpd,wd) {
##' @export
presc.single <- function(fn_data,stgs_alist,wd,mode,fn_cmpd_l,ppm_lim_fine=10,EIC_limit=0.001) {
no_drama_mkdir(wd)
- wd <- normalizePath(wd)
- gen_stgs_and_load(fn_data,stgs_alist,wd)
+ gen_stgs_and_load(stgs_alist,wd)
## Generate and load the compound list.
- x <- gen_cmpdl_and_load(fn_data,wd,fn_cmpd_l)
- fn_comp <- x$fn_cmpdl
+ x <- gen_cmpdl_and_load(wd,fn_cmpd_l)
+ fn_cmpd_l <- x$fn_cmpdl
n_cmpd <- x$n
## Generate file table.
@@ -173,7 +257,7 @@ presc.single <- function(fn_data,stgs_alist,wd,mode,fn_cmpd_l,ppm_lim_fine=10,EI
#curd <- setwd(wd)
res <-RMB_EIC_prescreen_df(wd=wd,RMB_mode=mode, FileList=fn_table,
- cmpd_list=fn_comp,
+ cmpd_list=fn_cmpd_l,
ppm_limit_fine=ppm_lim_fine,
EIC_limit=EIC_limit)
#setwd(curd)
@@ -181,146 +265,9 @@ presc.single <- function(fn_data,stgs_alist,wd,mode,fn_cmpd_l,ppm_lim_fine=10,EI
}
-##' Runs a compound mixture workflow on a single mzML file.
-##'
-##' @title RMassBank Spectral Workflow on a Single Compound Mixture
-##' @param fn_data A mzML data file.
-##' @param stgs_alist RMassBank settings. It can either be a named
-##' list of settings, or a filename of a YAML file.
-##' @param wd The name of the work directory.
-##' @param fn_cmpd_list The file name of he compound list
-##' corresponding to `fn_data`.
-##' @param mode Modes as described in the standard workflow vignette
-##' of RMassBank.
-##' @param readMethod Default read method is "mzR". Consult the
-##' documentation of `msmsRead` for details.
-##' @param archdir The directory to store R objects created during
-##' workflow execution.
-##' @param lastStep The last step in the workflow. Default is eight.
-##' @return MsmsWorkspace object.
-##' @author Todor Kondić
-sw.single<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="archive",lastStep=8) {
- ## Generate settings file and load.
- no_drama_mkdir(wd)
- wd <- normalizePath(wd)
- gen_stgs_and_load(fn_data,stgs_alist,wd)
-
- ## Generate and load the compound list.
- x <- gen_cmpdl_and_load(fn_data,wd,fn_cmpd_list)
- fn_comp <- x$fn_cmpdl
- n_cmpd <- x$n
-
- ## Generate file table.
- fn_table <- gen_file_table(fn_data,n_cmpd,wd)
-
- ## Make empty workspace.
- w <- RMassBank::newMsmsWorkspace()
- ## Run the workflow.
- message(paste("Reading in file:",fn_data))
- w <-RMassBank::msmsRead(w,filetable=fn_table,readMethod="mzR",mode=mode)
- archdir<-file.path(wd,archdir)
- no_drama_mkdir(archdir)
- fn_arch<-file.path(archdir,paste(basename(fn_data),".archive",sep=''))
- RMassBank::msmsWorkflow(w, mode=mode, steps=2:lastStep,archivename=fn_arch)
-}
-
-##' Runs the first step of the compound mixture workflow on a single mzML file.
-##'
-##' @title RMassBank Spectral Workflow on a Single Compound Mixture (step 1)
-##' @param fn_data A mzML data file.
-##' @param stgs_alist RMassBank settings. It can either be a named
-##' list of settings, or a filename of a YAML file.
-##' @param wd The name of the work directory.
-##' @param fn_cmpd_list The file name of he compound list
-##' corresponding to `fn_data`.
-##' @param mode Modes as described in the standard workflow vignette
-##' of RMassBank.
-##' @param readMethod Default read method is "mzR". Consult the
-##' documentation of `msmsRead` for details.
-##' @return MsmsWorkspace object.
-##' @author Todor Kondić
-sw.single.1 <- function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,
- readMethod="mzR") {
- ## Generate settings file and load.
- no_drama_mkdir(wd)
- wd <- normalizePath(wd)
- gen_stgs_and_load(fn_data,stgs_alist,wd)
-
- ## Generate and load the compound list.
- x <- gen_cmpdl_and_load(fn_data,wd,fn_cmpd_list)
- fn_comp <- x$fn_cmpdl
- n_cmpd <- x$n
-
- ## Generate file table.
- fn_table <- gen_file_table(fn_data,n_cmpd,wd)
-
- ## Make empty workspace.
- w <- RMassBank::newMsmsWorkspace()
- ## Run the workflow.
- message(paste("Reading in file:",fn_data))
- RMassBank::msmsRead(w,filetable=fn_table,readMethod="mzR",mode=mode)}
-
-##' Runs steps after sw.single.1 of compound mixture workflow on a
-##' single mzML file.
-##'
-##' @title RMassBank Spectral Workflow on a Single Compound Mixture (after step 1)
-##' @param w The msmsWorkspace object that was processed by
-##' sw.single.1.
-##' @param wd The current working dir.
-##' @param archdir The directory to store R objects created during
-##' workflow execution.
-##' @param lastStep The last step in the workflow. Default is eight.
-##' @return MsmsWorkspace object.
-##' @author Todor Kondić
-sw.single.next<-function(w,wd,archdir="archive",lastStep=8) {
-
- archdir<-file.path(wd,archdir)
- no_drama_mkdir(archdir)
- fn_arch<-file.path(archdir,paste(wd,".archive",sep=''))
- RMassBank::loadRmbSettings(file.path(wd,basename(wd),".mzML.ini"))
- RMassBank::loadList(file.path(wd,basename(wd),".mzML.comp.csv"))
- RMassBank::msmsWorkflow(w, mode=mode, steps=2:lastStep,archivename=fn_arch)
-}
-
-
-
-##' Prepare single mbWorkspace object based on the workspace, the
-##' infolist name and RMassBank settings.
-##'
-##'
-##' @title Prepare Single mbWorkspace object
-##' @param w MsmsWorkspace object.
-##' @param fn_info Filename of the infolist to be generated.
-##' @param fn_stgs Filename of the RMassBank settings.
-##' @return A mbWorkspace object.
-##' @author Todor Kondić
-mb.prep.single<-function(w,fn_info,fn_stgs) {
- RMassBank::loadRmbSettings(fn_stgs)
- mb <- RMassBank::newMbWorkspace(w)
- RMassBank::resetInfolists(mb)
- RMassBank::mbWorkflow(mb,infolist_path=fn_info)
-}
-##' Vectorize mb.prep function.
-##'
-##'
-##' @title Vectorized mb.prep function.
-##' @param w A sequence of msmsWorkspaces.
-##' @param fn_info A sequence of infolist filenams to be generated.
-##' @param fn_stgs A sequence of settings associated with each
-##' msmsWorkspace object.
-##' @return A list of mbWorkspaces.
-##' @author Todor Kondić
-mb.prep.v<-function(w,fn_info,fn_stgs) {
- f<-Vectorize(mb.prep.single,vectorize.args=c("w","fn_info","fn_stgs"),SIMPLIFY=F)
- res<-f(w,fn_info,fn_stgs)
- names(res)<-names(w)
- res
-}
-
##' Performs a single MassBank workflow after preparation.
##'
-##'
##' @title Single MassBank workflow.
##' @param mb A mbWorkspace object.
##' @param infodir Directory containing the infolist.
@@ -360,54 +307,6 @@ presc.v<-function(fn_data,fn_cmpd_l,mode,ppm_lim_fine=10,EIC_limit=0.001) {
f(fn_data,stgs_alist,wd,mode=mode,fn_cmpd_l=fn_cmpd_l,ppm_lim_fine=ppm_lim_fine,EIC_limit=EIC_limit)
}
-
-##' Interface to vectorised spectral workflow.
-##'
-##'
-##' @title Vectorised Spectral Workflow.
-##' @param fn_data A sequence of mzML input files.
-##' @param stgs_alist A list of named list of settings, or a list of
-##' filenames of YAML files containing the settings.
-##' @param wd The list of working directories.
-##' @param fn_cmpd_list The compound list characterising the mixtures.
-##' @param mode Same as in msmsRead.
-##' @param readMethod Same as in msmsRead.
-##' @param archdir Name of the archive.
-##' @param lastStep The last step of the spectral workflow.
-##' @param combine If TRUE, use combineMultiplicies to merge
-##' workspaces corresponding to different collisional energies.
-##' @return A named list of spectral workspaces. The names are derived
-##' from data filenames.
-##' @author Todor Kondić
-v<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="archive",lastStep=8,combine=F) {
- idir<-function(n) file.path(".",stripext(n))
- f<-Vectorize(sw.single,vectorize.args=c("wd","fn_data","stgs_alist"),SIMPLIFY=F)
- rootdir <- getwd()
- if (combine) {
- z<-f(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod=readMethod,archdir=archdir,lastStep=7)
- names(z)<-basename(fn_data)
- zz<-RMassBank::combineMultiplicities(z)
-
- combdir<-"combined"
- archdir<-file.path(rootdir,combdir,archdir)
- no_drama_mkdir(combdir)
- no_drama_mkdir(archdir)
- 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))
- names(res)<-paste(combdir,".mzML",sep='') #Clearly a hack.
- res
- } else {
- z<-f(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod=readMethod,archdir=archdir,lastStep=lastStep)
- names(z)<-basename(fn_data)
- z
- }
-}
-
##' Prescreens. Writes data out. Adapted from ReSOLUTION
##'
##'
@@ -605,62 +504,6 @@ presc.plot <- function(wd,out="prescreen.pdf",pal="Dark2",cex=0.75,digits=6) {
}
dev.off()
}
-
-
-
-
-
-##' Interface to parallel spectral workflow.
-##'
-##'
-##' @title Parallel Spectral Workflow.
-##' @param cl Cluster.
-##' @param fn_data A sequence of mzML input files.
-##' @param stgs_alist A list of named list of settings, or a list of
-##' filenames of YAML files containing the settings.
-##' @param wd The list of working directories.
-##' @param fn_cmpd_list The compound list characterising the mixtures.
-##' @param mode Same as in msmsRead.
-##' @param readMethod Same as in msmsRead.
-##' @param archdir Name of the archive.
-##' @param lastStep The last step in spectral workflow.
-##' @param combine If TRUE, use combineMultiplicies to merge
-##' workspaces corresponding to different collisional energies.
-##' @param combdest Combine destination directory.
-##' @return A named list of spectral workspaces. The names are derived
-##' from data filenames.
-##' @author Todor Kondić
-p.sw<-function(cl,fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="archive",lastStep=8,combine=F,combdest="combined") {
- idir<-function(n) file.path(".",stripext(n))
- fnocomb<-function(fn,stgs,wd) {
- sw.single(fn,stgs,wd,fn_cmpd_list,mode,readMethod,archdir,lastStep=lastStep)
- }
- fcomb <- function(fn,stgs,wd) sw.single(fn,stgs,wd,fn_cmpd_list,mode,readMethod,archdir,lastStep=7)
- if (combine) {
- z<-parallel::clusterMap(cl,fcomb,fn_data,stgs_alist,wd)
- names(z)<-basename(fn_data)
- zz<-RMassBank::combineMultiplicities(z)
- archdir<-file.path(combdest,archdir)
- no_drama_mkdir(combdest)
- no_drama_mkdir(archdir)
- fn_arch<-file.path(archdir,"archive")
- fn_comb_stgs <- file.path(combdest,paste(basename(combdest),".mzML.ini",sep=''))
- ## ddirs <- sapply(fn_data,idir)
- ## stgs_fls <- sapply(ddirs,function(x) file.path(x,paste(basename(x),".mzML.ini",sep='')))
- mk_combine_file(stgs_alist,fn_comb_stgs)
- anycpdlist <- file.path(wd[[1]],paste(basename(wd[[1]]),".mzML.comp.csv",sep=''))
- RMassBank::loadRmbSettings(fn_comb_stgs)
- RMassBank::loadList(anycpdlist)
- res<-list(RMassBank::msmsWorkflow(zz, steps=8, mode=mode, archivename = fn_arch))
- names(res)<-paste(basename(combdest),".ini",sep='') #Clearly a hack.
- res
- } else {
- z<-parallel::clusterMap(cl,fnocomb,fn_data,stgs_alist,wd)
- names(z)<-basename(fn_data)
- z
- }
-}
-
##' Interface to vectorised Mass Bank workflow.
##'
diff --git a/R/run.R b/R/run.R
index 7399854..76a1ac7 100644
--- a/R/run.R
+++ b/R/run.R
@@ -51,30 +51,61 @@ presc.do<-function(fn_data,fn_cmpd_list,mode,proc=F) {
##'
##' @title Perform MassBank Workflow on Multiple Compound Mixtures
##' @param fn_data List of mzML data filenames to be processed.
-##' @param fn_cmpd_list Compound list.
+##' @param fn_cmpd_l Compound list.
##' @param mode as in msmsRead.
##' @param dest The destination data directory.
##' @param combine If TRUE, use combineMultiplicies to merge
##' workspaces corresponding to different collisional energies.
##' @param proc Split work between this amount of processes. If FALSE
##' (or, 1), run sequential.
+##' @param split This is the last step before combine
##' @return A named list of msmsWorkspace objects.
##' @author Todor Kondić
##' @export
-sw.do<-function(fn_data,fn_cmpd_list,mode,dest=".",combine=F,proc=F) {
- dest <- normalizePath(dest)
- no_drama_mkdir(dest)
- fn_data <- normalizePath(fn_data)
- wdirs<-sapply(basename(fn_data),function(nm) file.path(dest,stripext(nm)))
- stgs<-sapply(fn_data,function (nm) file.path(paste(stripext(nm),"ini",sep='.')))
-
- if (proc) {
- cl<-parallel::makeCluster(proc)
- parallel::clusterEvalQ(cl,library("rmbmix"))
- p.sw(cl,fn_data,stgs,wdirs,fn_cmpd_list,mode,combine=combine)
- } else {
- v(fn_data,stgs,wdirs,fn_cmpd_list,mode,combine=combine)
+sw.do <- function(fn_data, fn_cmpd_l, mode, dest=".", combine=F,
+ proc=F,split=3) {
+
+ conf(fn_data,fn_cmpd_l,dest)
+ fread <- function(fn_data) {
+ wd <- fn_data2wd(fn_data,dest)
+ reconf(wd)
+ w <- RMassBank::newMsmsWorkspace()
+ RMassBank::msmsRead(w=w,filetable = get_ftable_fn(wd),
+ mode=mode,readMethod = "mzR")
}
+ fwork <- Vectorize(function(w,wd,steps) {
+ archdir <- file.path(wd,"archive")
+ no_drama_mkdir(archdir)
+ fn_arch <- file.path(archdir,"archive")
+ reconf(wd)
+ RMassBank::msmsWorkflow(w=w,mode=mode,steps=steps,archivename = fn_arch)
+ }, vectorize.args = c("w","wd"),SIMPLIFY=F)
+
+ w <- if (proc) {
+ cl=parallel::makeCluster(proc)
+ parallel::clusterEvalQ(cl,library(rmbmix))
+ parallel::clusterMap(cl,fread,fn_data)
+ } else {
+ lapply(fn_data,fread)
+ }
+ wd <- fn_data2wd(fn_data,dest)
+ w <- fwork(w,wd,steps=2:split)
+ if (combine) {
+ ## Combined workflow is not based on a single file, but the
+ ## functions that generate config are. Therefore, lets create
+ ## a fake filename.
+ fakefile <- "combine.mzML"
+ cwd <- fn_data2wd(fakefile,dest)
+ xx <- get_stgs_fn(wd[[1]])
+ file.copy(xx,"combine.ini",overwrite = T)
+ # mk_combine_file(get_stgs_fn(wd),"combine.ini")
+ conf(fakefile,fn_cmpd_l,dest)
+ reconf(cwd)
+ w <- list(RMassBank::combineMultiplicities(w))
+ wd <- list(cwd)
+ }
+ w <- fwork(w,wd,steps=(split+1):8)
+ names(w) <- wd
}
##' Creates and prepares mbWorkspace objects before the full workflow
@@ -85,17 +116,22 @@ sw.do<-function(fn_data,fn_cmpd_list,mode,dest=".",combine=F,proc=F) {
##'
##' @title Prepare mbWorkspace objects
##' @param w A list of spectral workspace inputs.
-##' @param rdir Data root.
-##' @param proc Split work between this amount of processes. If FALSE
##' @return Named list of prepared mbWorkspace objects.
##' @author Todor Kondić
##' @export
-mb.prep<-function(w,rdir=".") {
- idir<-function(n) file.path(rdir,stripext(n))
- sapply(names(w),function (n) no_drama_mkdir(file.path(idir(n),"info")))
- fn_info<-sapply(names(w),function (n) file.path(idir(n),"info",attch(n,'.info.csv')))
- fn_stgs<-sapply(names(w),function(n) file.path(idir(n),attch(n,'.ini')))
- mb.prep.v(w,fn_info,fn_stgs)
+mb.prep<-function(w) {
+ wd <- names(w)
+ fwork <- Vectorize(function(w,wd) {
+ reconf(wd)
+ idir <- gen_info_dir(wd)
+ mb <- RMassBank::newMbWorkspace(w)
+ RMassBank::resetInfolists(mb)
+ RMassBank::mbWorkflow(mb,infolist_path = get_info_fn(wd))
+ },vectorize.args = c("w","wd"))
+
+ mb <- fwork(w,wd)
+ names(mb) <- wd
+ mb
}
--
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