Streamline mix.R and run.R

More sensible (re)loading of the configuration files, encapsulation of
certain operations and other fixes

* mix.R(get_.*): Generate various filenames.

* mix.R(various intermediate wrappers around RMassBank calls):
  removed.

* run.R(presc.do): Adjust to changes in mix.R

* man: Update docs.

* NAMESPACE: Update exports.

NAMESPACE

@@ -3,8 +3,5 @@
 export(mb.do)
 export(mb.prep)
 export(presc.do)
-export(presc.p)
 export(presc.plot)
-export(presc.single)
-export(presc.v)
 export(sw.do)

R/mix.R

@@ -70,6 +70,9 @@ fn_data2wd <- function(fn_data,dest) {
     },vectorize.args="fn_data")
     f(fn_data)
 }
+
+get_presc_d <- function(wd) { file.path(wd,"prescreen")}
+gen_presc_d <- function(wd) { no_drama_mkdir(get_presc_d(wd))}
     
     
 
@@ -86,7 +89,7 @@ get_stgs_fn <- function(wd) {
 }
 
 get_ftable_fn <- function(wd) {
-    f <- function(wd) file.path(wd,"ftable.ini")
+    f <- function(wd) file.path(wd,"ftable.csv")
     fv <- Vectorize(f,vectorize.args=c("wd"))
     fv(wd)
 }
@@ -229,61 +232,6 @@ reconf <- function(wd) {## Load the settings.
     RMassBank::loadList(fn_cmpd_l)
 }
 
-##' Wrapper for a single prescreening call. Produces output in the
-##' usual mix method places.
-##'
-##' @title Wrapper for RMB_EIC_Prescreen
-##' @param fn_data The mzML filename.
-##' @param stgs_alist Settings named list, or a settings filename.
-##' @param wd Directory under which results are archived.
-##' @param mode RMB mode. 
-##' @param fn_cmpd_l Filename of the compound list.
-##' @param ppm_lim_fine The ppm_limit_fine argument to RMB_EIC_Prescreen
-##' @param EIC_limit Passed down to RMB_EIC_Prescreen.
-##' @return result of RMB_EIC_Prescreen
-##' @author Todor Kondić
-##' @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)
-    gen_stgs_and_load(stgs_alist,wd)
-    
-    ## Generate and load the compound list.
-    x <- gen_cmpdl_and_load(wd,fn_cmpd_l)
-    fn_cmpd_l <- x$fn_cmpdl
-    n_cmpd <- x$n
-
-    ## Generate file table.
-    fn_table <- gen_file_table(fn_data,n_cmpd,wd)
-
-    #curd <- setwd(wd)
-    res <-RMB_EIC_prescreen_df(wd=wd,RMB_mode=mode, FileList=fn_table,
-                               cmpd_list=fn_cmpd_l,
-                               ppm_limit_fine=ppm_lim_fine,
-                               EIC_limit=EIC_limit)
-    #setwd(curd)
-    res
-
-}
-
-##' Vectorises presc.single.
-##'
-##' @title Vectorises presc.single
-##' @param fn_data Sequence of mzML filenames.
-##' @param fn_cmpd_l Compound list filename.
-##' @param mode RMB mode.
-##' @param ppm_lim_fine Prescreen fine limit (see ReSOLUTION prescreening function).
-##' @param EIC_limit Prescreen EIC limit (see ReSOLUTION prescreening function).
-##' @return Nothing useful.
-##' @author Todor Kondić
-##' @export
-presc.v<-function(fn_data,fn_cmpd_l,mode,ppm_lim_fine=10,EIC_limit=0.001) {
-    idir<-function(n) file.path(".",stripext(n))
-    wd <- sapply(fn_data,idir)
-    stgs_alist <- sapply(wd,function(d) {paste(d,".ini",sep='')})
-    f<-Vectorize(presc.single,vectorize.args=c("fn_data","stgs_alist","wd"),SIMPLIFY=F)
-    f(fn_data,stgs_alist,wd,mode=mode,fn_cmpd_l=fn_cmpd_l,ppm_lim_fine=ppm_lim_fine,EIC_limit=EIC_limit)
-}
-
 ##' Prescreens. Writes data out. Adapted from ReSOLUTION
 ##'
 ##' 
@@ -367,33 +315,6 @@ RMB_EIC_prescreen_df <- function (wd, RMB_mode, FileList, cmpd_list,
               row.names = F)
 }
 
-
-
-##' Parallel version of presc.single.
-##'
-##' @title Parallel version of presc.single
-##' @param cl Cluster object.
-##' @param fn_data Sequence of mzML files.
-##' @param fn_cmpd_l Filename of the compound list.
-##' @param mode RMB mode.
-##' @param ppm_lim_fine See ReSOLUTION.
-##' @param EIC_limit See ReSOLUTION.
-##' @return Nothing useful.
-##' @author Todor Kondić
-##' @export
-presc.p<-function(cl,fn_data,fn_cmpd_l,mode,ppm_lim_fine=10,EIC_limit=0.001) {
-    idir<-function(n) file.path(".",stripext(n))
-    wd <- sapply(fn_data,idir)
-    stgs_alist <- sapply(wd,function(d) {paste(d,".ini",sep='')})
-
-    f <- function(fn_data,stgs_alist,wd) presc.single(fn_data=fn_data,stgs_alist=stgs_alist,wd=wd,mode=mode,
-                                                      fn_cmpd_l=fn_cmpd_l,ppm_lim_fine=ppm_lim_fine,EIC_limit=EIC_limit)
-    
-    parallel::clusterMap(cl,fun=f,fn_data,stgs_alist,wd)
-    
-}
-
-
 ##' Plot the output of prescreen.
 ##'
 ##' @title Plot the Output of Prescreen
@@ -414,7 +335,7 @@ presc.plot <- function(wd,out="prescreen.pdf",pal="Dark2",cex=0.75,digits=6) {
     for (i in seq(length(eics))) {
         eic <- eics[[i]]
         maybekid <- maybekids[[i]]
-        fn_ini <- lapply(wd,function(x) file.path(x,list.files(path=x,patt="*.ini")[[1]]))
+        fn_ini <- lapply(wd,get_stgs_fn)
         
         lbls <- lapply(fn_ini,function(x) {s <- yaml::yaml.load_file(x);s$spectraList[[1]]$ce})
         plot.new()

R/run.R

@@ -13,20 +13,34 @@ attch<-function(...) paste(...,sep='')
 ##' @title Prescreening on bunch of files.
 ##' @param fn_data The mzML files. Basis for the out directory name
 ##'     generation.
-##' @param fn_cmpd_list The compound list CSV.
+##' @param fn_cmpd_l The compound list.
 ##' @param mode RMB mode.
+##' @param dest Destination directory.
 ##' @param proc Amount of processors, or FALSE. 
+##' @param fn_cmpd_list The compound list CSV.
 ##' @return Nothing useful.
 ##' @author Todor Kondić
 ##' @export
-presc.do<-function(fn_data,fn_cmpd_list,mode,proc=F) {
+presc.do<-function(fn_data,fn_cmpd_l,mode,dest=".",proc=F,...) {
+    conf(fn_data,fn_cmpd_l,dest)
 
+    fread <- function(fn_data) {
+        wd <- fn_data2wd(fn_data,dest)
+        gen_presc_d(wd)
+        reconf(wd)
+        message("Currently processing: ",wd)
+        fn_ftable <- get_ftable_fn(wd)
+        fn_cmpd_l <- get_cmpd_l_fn(wd)
+        RMB_EIC_prescreen_df(wd=wd,RMB_mode=mode,FileList=fn_ftable,
+                             cmpd_list=fn_cmpd_l,...)
+    }
 
     if (proc) {
-        cl<-parallel::makeCluster(proc,type='FORK')
-        presc.p(cl=cl,fn_data,fn_cmpd_l=fn_cmpd_list,mode=mode)
+        cl<-parallel::makeCluster(proc)
+        parallel::clusterEvalQ(cl,library(rmbmix))
+        parallel::clusterMap(cl,fread,fn_data)
     } else {
-        presc.v(fn_data,fn_cmpd_l=fn_cmpd_list,mode)
+        lapply(fn_data,fread)
     }
 }
 

man/gen_comp_list.Rd → man/gen_cmpd_l.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/mix.R
-\name{gen_comp_list}
-\alias{gen_comp_list}
+\name{gen_cmpd_l}
+\alias{gen_cmpd_l}
 \title{Generate Compound List File}
 \usage{
-gen_comp_list(src_fn, dest_fn)
+gen_cmpd_l(src_fn, dest_fn)
 }
 \arguments{
 \item{src_fn}{The input compound list CSV filename.}

man/gen_cmpdl_and_load.Rd

@@ -4,12 +4,12 @@
 \alias{gen_cmpdl_and_load}
 \title{Generate and Load the RMassBank Compound List}
 \usage{
-gen_cmpdl_and_load(fn_data, wd, fn_cmpdl)
+gen_cmpdl_and_load(wd, fn_cmpdl)
 }
 \arguments{
-\item{fn_data}{The mzML filename.}
-
 \item{wd}{Directory under which results are archived.}
+
+\item{fn_cmpdl}{The input compound list filename.}
 }
 \value{
 Named list. The key \code{fn_cmpdl} is the path of the

man/gen_file_table.Rd → man/gen_ftable.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/mix.R
-\name{gen_file_table}
-\alias{gen_file_table}
+\name{gen_ftable}
+\alias{gen_ftable}
 \title{Generate and Load the RMassBank Settings File}
 \usage{
-gen_file_table(fn_data, n_cmpd, wd)
+gen_ftable(fn_data, wd, n_cmpd)
 }
 \arguments{
 \item{fn_data}{The mzML filename.}
 
-\item{n_cmpd}{Number of compounds.}
-
 \item{wd}{Directory under which results are archived.}
+
+\item{n_cmpd}{Number of compounds.}
 }
 \value{
 File path of the file table.

man/gen_stgs_and_load.Rd

@@ -4,11 +4,9 @@
 \alias{gen_stgs_and_load}
 \title{Generate and Load the RMassBank Settings File}
 \usage{
-gen_stgs_and_load(fn_data, stgs, wd)
+gen_stgs_and_load(stgs, wd)
 }
 \arguments{
-\item{fn_data}{The mzML filename.}
-
 \item{stgs}{Settings named list, or a settings filename.}
 
 \item{wd}{Directory under which results are archived.}

man/mb.do.Rd

@@ -4,13 +4,11 @@
 \alias{mb.do}
 \title{Perform the Mass Bank workflow}
 \usage{
-mb.do(mb, rdir = ".", proc = F)
+mb.do(mb, proc = F)
 }
 \arguments{
 \item{mb}{The list of prepared mbWorkspace objects.}
 
-\item{rdir}{Root data dir.}
-
 \item{proc}{Split work between this amount of processes. If FALSE
 (or, 1), run sequential.}
 }

man/mb.prep.Rd

@@ -4,14 +4,10 @@
 \alias{mb.prep}
 \title{Prepare mbWorkspace objects}
 \usage{
-mb.prep(w, rdir = ".")
+mb.prep(w)
 }
 \arguments{
 \item{w}{A list of spectral workspace inputs.}
-
-\item{rdir}{Data root.}
-
-\item{proc}{Split work between this amount of processes. If FALSE}
 }
 \value{
 Named list of prepared mbWorkspace objects.

man/mb.prep.single.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mb.prep.single}
-\alias{mb.prep.single}
-\title{Prepare Single mbWorkspace object}
-\usage{
-mb.prep.single(w, fn_info, fn_stgs)
-}
-\arguments{
-\item{w}{MsmsWorkspace object.}
-
-\item{fn_info}{Filename of the infolist to be generated.}
-
-\item{fn_stgs}{Filename of the RMassBank settings.}
-}
-\value{
-A mbWorkspace object.
-}
-\description{
-Prepare single mbWorkspace object based on the workspace, the
-infolist name and RMassBank settings.
-}
-\author{
-Todor Kondić
-}

man/mb.prep.v.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mb.prep.v}
-\alias{mb.prep.v}
-\title{Vectorized mb.prep function.}
-\usage{
-mb.prep.v(w, fn_info, fn_stgs)
-}
-\arguments{
-\item{w}{A sequence of msmsWorkspaces.}
-
-\item{fn_info}{A sequence of infolist filenams to be generated.}
-
-\item{fn_stgs}{A sequence of settings associated with each
-msmsWorkspace object.}
-}
-\value{
-A list of mbWorkspaces.
-}
-\description{
-Vectorize mb.prep function.
-}
-\author{
-Todor Kondić
-}

man/mb.single.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mb.single}
-\alias{mb.single}
-\title{Single MassBank workflow.}
-\usage{
-mb.single(mb, infodir, fn_stgs)
-}
-\arguments{
-\item{mb}{A mbWorkspace object.}
-
-\item{infodir}{Directory containing the infolist.}
-
-\item{fn_stgs}{The settings associated with the mbWorkspace
-object.}
-}
-\value{
-A mbWorkflow object.
-}
-\description{
-Performs a single MassBank workflow after preparation.
-}
-\author{
-Todor Kondić
-}

man/no_drama_mkdir.Rd

@@ -7,7 +7,7 @@
 no_drama_mkdir(path)
 }
 \arguments{
-\item{path}{Name of the directory.}
+\item{path}{Names of the directories.}
 }
 \value{
 The character string containing the input argument \code{path}.

man/p.sw.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{p.sw}
-\alias{p.sw}
-\title{Parallel Spectral Workflow.}
-\usage{
-p.sw(cl, fn_data, stgs_alist, wd, fn_cmpd_list, mode, readMethod = "mzR",
-  archdir = "archive", lastStep = 8, combine = F,
-  combdest = "combined")
-}
-\arguments{
-\item{cl}{Cluster.}
-
-\item{fn_data}{A sequence of mzML input files.}
-
-\item{stgs_alist}{A list of named list of settings, or a list of
-filenames of YAML files containing the settings.}
-
-\item{wd}{The list of working directories.}
-
-\item{fn_cmpd_list}{The compound list characterising the mixtures.}
-
-\item{mode}{Same as in msmsRead.}
-
-\item{readMethod}{Same as in msmsRead.}
-
-\item{archdir}{Name of the archive.}
-
-\item{lastStep}{The last step in spectral workflow.}
-
-\item{combine}{If TRUE, use combineMultiplicies to merge
-workspaces corresponding to different collisional energies.}
-
-\item{combdest}{Combine destination directory.}
-}
-\value{
-A named list of spectral workspaces. The names are derived
-from data filenames.
-}
-\description{
-Interface to parallel spectral workflow.
-}
-\author{
-Todor Kondić
-}

man/presc.do.Rd

@@ -4,17 +4,21 @@
 \alias{presc.do}
 \title{Prescreening on bunch of files.}
 \usage{
-presc.do(fn_data, fn_cmpd_list, mode, proc = F)
+presc.do(fn_data, fn_cmpd_l, mode, dest = ".", proc = F, ...)
 }
 \arguments{
 \item{fn_data}{The mzML files. Basis for the out directory name
 generation.}
 
-\item{fn_cmpd_list}{The compound list CSV.}
+\item{fn_cmpd_l}{The compound list.}
 
 \item{mode}{RMB mode.}
 
+\item{dest}{Destination directory.}
+
 \item{proc}{Amount of processors, or FALSE.}
+
+\item{fn_cmpd_list}{The compound list CSV.}
 }
 \value{
 Nothing useful.

man/presc.p.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.p}
-\alias{presc.p}
-\title{Parallel version of presc.single}
-\usage{
-presc.p(cl, fn_data, fn_cmpd_l, mode, ppm_lim_fine = 10,
-  EIC_limit = 0.001)
-}
-\arguments{
-\item{cl}{Cluster object.}
-
-\item{fn_data}{Sequence of mzML files.}
-
-\item{fn_cmpd_l}{Filename of the compound list.}
-
-\item{mode}{RMB mode.}
-
-\item{ppm_lim_fine}{See ReSOLUTION.}
-
-\item{EIC_limit}{See ReSOLUTION.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Parallel version of presc.single.
-}
-\author{
-Todor Kondić
-}

man/presc.single.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.single}
-\alias{presc.single}
-\title{Wrapper for RMB_EIC_Prescreen}
-\usage{
-presc.single(fn_data, stgs_alist, wd, mode, fn_cmpd_l, ppm_lim_fine = 10,
-  EIC_limit = 0.001)
-}
-\arguments{
-\item{fn_data}{The mzML filename.}
-
-\item{stgs_alist}{Settings named list, or a settings filename.}
-
-\item{wd}{Directory under which results are archived.}
-
-\item{mode}{RMB mode.}
-
-\item{fn_cmpd_l}{Filename of the compound list.}
-
-\item{ppm_lim_fine}{The ppm_limit_fine argument to RMB_EIC_Prescreen}
-
-\item{EIC_limit}{Passed down to RMB_EIC_Prescreen.}
-}
-\value{
-result of RMB_EIC_Prescreen
-}
-\description{
-Wrapper for a single prescreening call. Produces output in the
-usual mix method places.
-}
-\author{
-Todor Kondić
-}

man/presc.v.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.v}
-\alias{presc.v}
-\title{Vectorises presc.single}
-\usage{
-presc.v(fn_data, fn_cmpd_l, mode, ppm_lim_fine = 10, EIC_limit = 0.001)
-}
-\arguments{
-\item{fn_data}{Sequence of mzML filenames.}
-
-\item{fn_cmpd_l}{Compound list filename.}
-
-\item{mode}{RMB mode.}
-
-\item{ppm_lim_fine}{Prescreen fine limit (see ReSOLUTION prescreening function).}
-
-\item{EIC_limit}{Prescreen EIC limit (see ReSOLUTION prescreening function).}
-}
-\value{
-Nothing useful.
-}
-\description{
-Vectorises presc.single.
-}
-\author{
-Todor Kondić
-}

man/sw.do.Rd

@@ -4,12 +4,13 @@
 \alias{sw.do}
 \title{Perform MassBank Workflow on Multiple Compound Mixtures}
 \usage{
-sw.do(fn_data, fn_cmpd_list, mode, dest = ".", combine = F, proc = F)
+sw.do(fn_data, fn_cmpd_l, mode, dest = ".", combine = F, proc = F,
+  split = 3)
 }
 \arguments{
 \item{fn_data}{List of mzML data filenames to be processed.}
 
-\item{fn_cmpd_list}{Compound list.}
+\item{fn_cmpd_l}{Compound list.}
 
 \item{mode}{as in msmsRead.}
 
@@ -20,6 +21,8 @@ workspaces corresponding to different collisional energies.}
 
 \item{proc}{Split work between this amount of processes. If FALSE
 (or, 1), run sequential.}
+
+\item{split}{This is the last step before combine}
 }
 \value{
 A named list of msmsWorkspace objects.

man/sw.single.1.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{sw.single.1}
-\alias{sw.single.1}
-\title{RMassBank Spectral Workflow on a Single Compound Mixture (step 1)}
-\usage{
-sw.single.1(fn_data, stgs_alist, wd, fn_cmpd_list, mode,
-  readMethod = "mzR")
-}
-\arguments{
-\item{fn_data}{A mzML data file.}
-
-\item{stgs_alist}{RMassBank settings. It can either be a named
-list of settings, or a filename of a YAML file.}
-
-\item{wd}{The name of the work directory.}
-
-\item{fn_cmpd_list}{The file name of he compound list
-corresponding to \code{fn_data}.}
-
-\item{mode}{Modes as described in the standard workflow vignette
-of RMassBank.}
-
-\item{readMethod}{Default read method is "mzR". Consult the
-documentation of \code{msmsRead} for details.}
-}
-\value{
-MsmsWorkspace object.
-}
-\description{
-Runs the first step of the compound mixture workflow on a single mzML file.
-}
-\author{
-Todor Kondić
-}