From 416d2ec39c51e2d0ee6c9be70b3b9e2271bce706 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Mon, 16 Jan 2023 09:27:38 +0100
Subject: [PATCH] mefrag, errors, test: Complete the system for running MetFrag
on `summ' entries.
* metfrag(metrag_run): Update.
---
R/errors.R | 6 ++++++
R/metfrag.R | 21 +++++++++++++++++----
tests/testthat/_snaps/metfrag.md | 24 ++++++++++++++++++++++++
tests/testthat/test-metfrag.R | 23 ++++++++++++++++-------
4 files changed, 63 insertions(+), 11 deletions(-)
diff --git a/R/errors.R b/R/errors.R
index 7b9493f..53f048e 100644
--- a/R/errors.R
+++ b/R/errors.R
@@ -31,3 +31,9 @@ check_file_absent <- function(file,what) {
check_not_one <- function(value,what) {
if (length(value)!=1L) stop(errorCondition(paste0("Size of", what, " is not one."), class=paste0(what,'-not-one')))
}
+
+check_extension <- function(extfileval,what) {
+ check_notastring(extfileval[[1]],what = what)
+ if (extfileval[[1]]==extfileval[[2]]) stop(errorCondition(paste0("We could not find the extension for ",what, ". The returned value was: ", extfileval[[2]]),
+ class = paste0(what,'-no-ext-found')))
+}
diff --git a/R/metfrag.R b/R/metfrag.R
index 93630f6..da543d0 100644
--- a/R/metfrag.R
+++ b/R/metfrag.R
@@ -41,7 +41,7 @@ metfrag_get_ms2_spec <- function(ms2,stag_entry) {
x
}
-metfrag_run <- function(param,path,subpaths,db_path,stag_tab,ms2,runtime,java_bin) {
+metfrag_run <- function(param,path,subpaths,db_path,stag_tab,ms2,runtime,java_bin,nproc = 1L) {
keys = intersect(colnames(stag_tab),colnames(ms2))
message("Generating MetFrag configs.")
file_tab = ms2[stag_tab,{
@@ -60,8 +60,21 @@ metfrag_run <- function(param,path,subpaths,db_path,stag_tab,ms2,runtime,java_bi
withr::with_dir(path,{
metfrag_run_many(fn_jar = runtime,
file_tab = file_tab,
- java_bin = java_bin)
+ java_bin = java_bin,
+ nproc = nproc)
})
+
+ ## We don't know (so well) in advance what are the endings of the
+ ## results files. Lets find this out.
+ pth = file.path(path,subpaths[["results"]])
+ a_res_f = list.files(path = pth,
+ pattern = param$SampleName)[[1]]
+ ext = sub(pattern = r"(^.*\.([[:alnum:]]+)$)",r"(\1)", a_res_f)
+ check_extension(c(ext=ext,file=a_res_f),what="mf-res-file")
+ file_tab[,f_res:=paste0(param$SampleName,"_",stag,".",(ext))]
+
+
+
}
@@ -203,7 +216,8 @@ metfrag_run_many_w_futures <- function(fn_jar,fn_conf,fn_log, mem = NA_character
metfrag_run_many <- function(fn_jar,file_tab, mem = NA_character_, java_bin = "java",nproc=1L) {
ntasks = NROW(file_tab)
- k = ntasks %/% nproc
+ todo = min(nproc,ntasks)
+ k = ntasks %/% todo
ndone = 0L
lc = 1L
while (ndone < ntasks) {
@@ -212,7 +226,6 @@ metfrag_run_many <- function(fn_jar,file_tab, mem = NA_character_, java_bin = "j
for (i in (ndone + 1):ncurr_last) {
fn_conf = file_tab[i,f_conf]
fn_log = file_tab[i,f_log]
- message("fn_conf:", fn_conf)
procs[[i-ndone]] = metfrag_run_one(fn_jar,
fn_conf= fn_conf,
fn_log = fn_log,
diff --git a/tests/testthat/_snaps/metfrag.md b/tests/testthat/_snaps/metfrag.md
index 2f4c222..5c7749d 100644
--- a/tests/testthat/_snaps/metfrag.md
+++ b/tests/testthat/_snaps/metfrag.md
@@ -18,3 +18,27 @@
[13] "MetFragDatabaseType = \nFragmentPeakMatchAbsoluteMassDeviation = 0.001\nFragmentPeakMatchRelativeMassDeviation = 5\nDatabaseSearchRelativeMassDeviation = 5\nMetFragScoreTypes = FragmenterScore,OfflineIndividualMoNAScore\nMetFragScoreWeights = 1,1\nMetFragCandidateWriter = CSV\nSampleName = sample_a_[M+]+_a\nMaximumTreeDepth = 2\nMetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter,IsotopeFilter\nMetFragPostProcessingCandidateFilter = InChIKeyFilter\nIonizedPrecursorMass = 777.7789\nIsPositiveIonMode = True\nPrecursorIonMode = 0\nResultsPath = results\nPeakListPath = spec/sample_a_[M+]+_a.csv\n\n"
[14] "MetFragDatabaseType = \nFragmentPeakMatchAbsoluteMassDeviation = 0.001\nFragmentPeakMatchRelativeMassDeviation = 5\nDatabaseSearchRelativeMassDeviation = 5\nMetFragScoreTypes = FragmenterScore,OfflineIndividualMoNAScore\nMetFragScoreWeights = 1,1\nMetFragCandidateWriter = CSV\nSampleName = sample_a_[M-]-_a\nMaximumTreeDepth = 2\nMetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter,IsotopeFilter\nMetFragPostProcessingCandidateFilter = InChIKeyFilter\nIonizedPrecursorMass = 777.7789\nIsPositiveIonMode = False\nPrecursorIonMode = 0\nResultsPath = results\nPeakListPath = spec/sample_a_[M-]-_a.csv\n\n"
+# function metfrag_run returns correct result.
+
+ Code
+ ftab
+ Output
+ ID adduct tag an CE
+ 1: 100 [M+H]+ AA 5413 10
+ 2: 100 [M+H]+ KO 5434 10
+ f_conf
+ 1: config/testsample_setNTs_ID100_adduct[M+H]+_tagAA_an5413.conf
+ 2: config/testsample_setNTs_ID100_adduct[M+H]+_tagKO_an5434.conf
+ f_log
+ 1: log/testsample_setNTs_ID100_adduct[M+H]+_tagAA_an5413.log
+ 2: log/testsample_setNTs_ID100_adduct[M+H]+_tagKO_an5434.log
+ f_spec
+ 1: spec/testsample_setNTs_ID100_adduct[M+H]+_tagAA_an5413.csv
+ 2: spec/testsample_setNTs_ID100_adduct[M+H]+_tagKO_an5434.csv
+ stag
+ 1: setNTs_ID100_adduct[M+H]+_tagAA_an5413
+ 2: setNTs_ID100_adduct[M+H]+_tagKO_an5434
+ f_res
+ 1: testsample_setNTs_ID100_adduct[M+H]+_tagAA_an5413.csv
+ 2: testsample_setNTs_ID100_adduct[M+H]+_tagKO_an5434.csv
+
diff --git a/tests/testthat/test-metfrag.R b/tests/testthat/test-metfrag.R
index 45abcaf..d05ef02 100644
--- a/tests/testthat/test-metfrag.R
+++ b/tests/testthat/test-metfrag.R
@@ -54,13 +54,22 @@ ok_return_val("metfrag_run",{
withr::with_dir(m$run$metfrag$path,{
stagtab = metfrag_get_stag_tab(m$out$tab$summ[ms2_sel == T])
- metfrag_run(param = m$conf$metfrag$param,
- path = m$run$metfrag$path,
- subpaths = m$run$metfrag$subpaths,
- db_path = m$run$metfrag$db_path,
- stag_tab = stab, ms2 = m$extr$ms2,
- runtime=m$run$metfrag$runtime,
- java_bin=m$run$metfrag$java_bin)
+ ftab = metfrag_run(param = m$conf$metfrag$param,
+ path = m$run$metfrag$path,
+ subpaths = m$run$metfrag$subpaths,
+ db_path = m$run$metfrag$db_path,
+ stag_tab = stagtab, ms2 = m$extr$ms2,
+ runtime=m$run$metfrag$runtime,
+ java_bin=m$run$metfrag$java_bin,
+ nproc = 2)
+
+ expect_snapshot(ftab)
+
+ for (f in ftab[,f_res]) {
+ expect_true(file.exists(file.path(m$run$metfrag$path,
+ m$run$metfrag$subpaths['results'],
+ f)))
+ }
})
--
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