diff create_sqlite_db.R @ 0:fe7d7cc95ca5 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_sqlite_db.R	Tue Mar 27 06:03:50 2018 -0400
@@ -0,0 +1,145 @@
+library(msPurity)
+library(optparse)
+library(xcms)
+library(CAMERA)
+print('CREATING DATABASE')
+
+
+xset_pa_filename_fix <- function(opt, pa, xset){
+
+
+  if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
+    # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables 
+    # needs to be done due to Galaxy moving the files around and screwing up any links to files
+
+    filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
+    filepaths <- filepaths[filepaths != ""]
+    new_names <- basename(filepaths)
+
+    galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
+    galaxy_names <- galaxy_names[galaxy_names != ""]
+
+    nsave <- names(pa@fileList)
+    old_filenames  <- basename(pa@fileList)
+    pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
+    names(pa@fileList) <- nsave
+
+    pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
+    pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
+  }
+
+
+ if(!all(basename(pa@fileList)==basename(xset@filepaths))){
+    if(!all(names(pa@fileList)==basename(xset@filepaths))){
+       print('FILELISTS DO NOT MATCH')
+       message('FILELISTS DO NOT MATCH')
+       quit(status = 1)
+    }else{
+      xset@filepaths <- unname(pa@fileList)
+    }
+  }
+
+
+  return(list(pa, xset))
+}
+
+
+
+option_list <- list(
+  make_option(c("-o", "--out_dir"), type="character"),
+  make_option("--pa", type="character"),
+  make_option("--xset_xa", type="character"),
+  make_option("--xcms_camera_option", type="character"),
+  make_option("--eic", action="store_true"),
+  make_option("--cores", default=4),
+  make_option("--mzML_files", type="character"),
+  make_option("--galaxy_names", type="character"),
+  make_option("--grp_peaklist", type="character"),
+  make_option("--db_name", type="character", default='lcms_data.sqlite'),
+  make_option("--raw_rt_columns", action="store_true")
+)
+
+# store options
+opt<- parse_args(OptionParser(option_list=option_list))
+
+loadRData <- function(rdata_path, name){
+  #loads an RData file, and returns the named xset object if it is there
+  load(rdata_path)
+  return(get(ls()[ls() == name]))
+}
+
+print(paste('pa', opt$pa))
+print(opt$xset)
+print(opt$xcms_camera_option)
+# Requires
+pa <- loadRData(opt$pa, 'pa')
+
+print('TESTETSTESTETE')
+print(pa@fileList)
+
+
+if (opt$xcms_camera_option=='xcms'){
+  xset <- loadRData(opt$xset, 'xset')
+  fix <- xset_pa_filename_fix(opt, pa, xset)  
+  pa <- fix[[1]]
+  xset <- fix[[2]]
+  xa <- NULL
+}else{
+  
+  xa <- loadRData(opt$xset, 'xa')
+  fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)  
+  pa <- fix[[1]]
+  xa@xcmsSet <- fix[[2]]
+  xset <- NULL
+}
+
+
+
+
+
+if(is.null(opt$grp_peaklist)){
+  grp_peaklist = NA
+}else{
+  grp_peaklist = opt$grp_peaklist
+}
+
+
+print(pa@fileList)
+print(xset@filepaths)
+
+
+db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
+                          grp_peaklist=grp_peaklist, db_name=opt$db_name)
+
+
+if (!is.null(opt$eic)){
+  if (is.null(opt$raw_rt_columns)){
+    rtrawColumns <- FALSE
+  }else{
+    rtrawColumns <- TRUE
+  }
+
+  # Saves the EICS into the previously created database
+  px <- msPurity::purityX(xset, saveEIC = TRUE,
+                           cores=opt$cores, sqlitePth=db_pth,
+                           rtrawColumns = rtrawColumns)
+}
+
+
+
+con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)
+
+cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
+             'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
+             'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ',
+             'FROM c_peak_groups AS cpg ',
+             'LEFT JOIN c_peak_X_c_peak_group AS cXg ON cXg.grpid=cpg.grpid ',
+             'LEFT JOIN c_peaks on c_peaks.cid=cXg.cid ',
+             'LEFT JOIN c_peak_X_s_peak_meta AS cXs ON cXs.cid=c_peaks.cid ',
+             'LEFT JOIN s_peak_meta ON cXs.pid=s_peak_meta.pid ',
+             'LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid')
+
+print(cmd)
+cpeakgroup_msms <- DBI::dbGetQuery(con, cmd)
+
+write.table(cpeakgroup_msms, file.path(opt$out_dir, 'cpeakgroup_msms.tsv'), row.names=FALSE, sep='\t')