--- a/create_sqlite_db.R	Wed Jul 18 06:04:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,239 +0,0 @@
-library(msPurity)
-library(optparse)
-library(xcms)
-library(CAMERA)
-print(sessionInfo())
-print('CREATING DATABASE')
-
-
-xset_pa_filename_fix <- function(opt, pa, xset){
-  print(xset@filepaths)
-
-  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)
-    }
-  }
-
-
-print(xset@phenoData)
-print(xset@filepaths)
-
-  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"),
-  make_option("--metfrag_result", type="character"),
-  make_option("--sirius_csifingerid_result", type="character"),
-  make_option("--probmetab_result", type="character")
-)
-
-
-# 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(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$grp_peaklist
-}
-
-
-
-db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
-                          grp_peaklist=grp_peaklist, db_name=opt$db_name)
-
-print(db_pth)
-
-if (!is.null(opt$eic)){
-  if (is.null(opt$raw_rt_columns)){
-    rtrawColumns <- FALSE
-  }else{
-    rtrawColumns <- TRUE
-  }
-  if (is.null(xset)){
-      xset <- xa@xcmsSet
-  }
-  # previous check should have matched filelists together
-  xset@filepaths <- unname(pa@fileList)
-
-  # Saves the EICS into the previously created database
-  px <- msPurity::purityX(xset, saveEIC = TRUE,
-                           cores=1, sqlitePth=db_pth,
-                           rtrawColumns = rtrawColumns)
-}
-
-con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)
-
-add_extra_table_elucidation <- function(name, pth, db_con){
-    if (is.null(pth)){
-        return(0)
-    } 
-
-    
-    DBI::dbWriteTable(conn=db_con, name=name, value=pth, sep='\t', header=T)
-
-
-}
-
-write_to_table <- function(df, db_con, name, append){
-
-       df <- df[!df$UID=='UID',]
-        print(filter_Score)
-        print(filter_Rank)
-        print('filter rank and score')
-
-
-        # get peakid, an scan id
-        df_ids <- stringr::str_split_fixed(df$UID, '-', 3)
-        colnames(df_ids) <- c('grp_id', 'file_id', 'pid')
-        df <- cbind(df_ids, df)
-        DBI::dbWriteTable(db_con, name=name, value=df, row.names=FALSE, append=append)
-}
-
-add_probmetab <- function(pth, xset, con){
-  if (!is.null(pth)){
-
-      df <- read.table(pth,  header = TRUE, sep='\t', stringsAsFactors = FALSE,  comment.char = "")
-      df$grp_id <- match(df$name, xcms::groupnames(xset))
-      start <- T 
-      for (i in 1:nrow(df)){
-
-         x <- df[i,]
-
-
-         if(is.na(x$proba) | x$proba =='NA'){
-
-	   next
-         }
-  
-         mpc <- stringr::str_split(x$mpc, ';')
-         proba <- stringr::str_split(x$proba, ';') 
-
-         for (j in 1:length(mpc[[1]])){
-    
-            row <-  c(x$grp_id, x$propmz, mpc[[1]][j], proba[[1]][j])
-           
-            if (start){
-               df_out <- data.frame(t(row), stringsAsFactors=F)
-               start <- F
-            }else{
-               df_out <- data.frame(rbind(df_out, row), stringsAsFactors=F)
-            }
-            print(df_out)
-
-         } 
-          
-     }
-
-     colnames(df_out) <- c('grp_id', 'propmz', 'mpc', 'proba')
-     DBI::dbWriteTable(con, name='probmetab_results', value=df_out, row.names=FALSE)
-
-  }
-
-
-}
-
-add_extra_table_elucidation('metfrag_results', opt$metfrag_result, con)
-add_extra_table_elucidation('sirius_csifingerid_results', opt$sirius_csifingerid_result, con)
-
-
-if (is.null(xset)){
-  DBI::dbWriteTable(con, name='xset_classes', value=xa@xcmsSet@phenoData, row.names=TRUE)
-  add_probmetab(opt$probmetab_result, xa@xcmsSet,  con)
-}else{
-
-  DBI::dbWriteTable(con, name='xset_classes', value=xset@phenoData, row.names=TRUE)
-  add_probmetab(opt$probmetab_result, xset,  con)
-
-}
-
-cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
-             'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
-             'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ',
-             'FROM c_peak_groups AS cpg ',
-             'LEFT JOIN c_peak_X_c_peak_group AS cXg ON cXg.grpid=cpg.grpid ',
-             'LEFT JOIN c_peaks on c_peaks.cid=cXg.cid ',
-             'LEFT JOIN c_peak_X_s_peak_meta AS cXs ON cXs.cid=c_peaks.cid ',
-             'LEFT JOIN s_peak_meta ON cXs.pid=s_peak_meta.pid ',
-             'LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid')
-
-print(cmd)
-cpeakgroup_msms <- DBI::dbGetQuery(con, cmd)
-
-write.table(cpeakgroup_msms, file.path(opt$out_dir, 'cpeakgroup_msms.tsv'), row.names=FALSE, sep='\t')