Mercurial > repos > tomnl > assess_purity_msms

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/backup_sqlite.R	Thu May 31 11:23:09 2018 -0400
@@ -0,0 +1,280 @@
+library(msPurity)
+library(optparse)
+library(xcms)
+library(CAMERA)
+print(sessionInfo())
+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"),
+  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$raw_rt_columns)){
+    rtrawColumns <- FALSE
+  }else{
+    rtrawColumns <- TRUE
+  }
+  if (is.null(xset)){
+      xset <- xa@xcmsSet
+  }
+  # previous check should have matched filelists together
+  xset@filepaths <- unname(pa@fileList)
+
+  # Saves the EICS into the previously created database
+  px <- msPurity::purityX(xset, saveEIC = TRUE,
+                           cores=1, sqlitePth=db_pth,
+                           rtrawColumns = rtrawColumns)
+}
+
+con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)
+
+add_extra_table_elucidation <- function(name, pth, db_con, filter_Score=NA, filter_Rank=NA){
+    if (is.null(pth)){
+        return(0)
+    }
+    chunk=50
+    c = 1
+    header_s = FALSE
+    con = file(pth, "r")
+     while ( TRUE ) {
+      line = readLines(con, n = 1)
+      print(line)
+      if ( length(line) == 0 ) {
+       break
+      }
+      line_v <- unlist(strsplit(line, split="\t"))
+      if (!header_s){
+       header = line_v
+       header_s = TRUE
+       df <- data.frame(ncol=length(header), nrow=0)
+       print(header)
+       colnames(df) <- header
+       df_blank <- df
+       print('CHECK')
+       write_to_table(df, db_con, name, FALSE, NA, NA)
+      }
+      print(line_v)
+
+       if (!is.na(filter_Score)){
+           if (line_v[header=='Score']<filter_Score){
+		next
+       	   }
+       }
+        if (!is.na(filter_Rank)){
+
+           if (line_v[header=='Rank']>filter_Rank){
+		next
+       	   }
+        }
+
+      df <- rbind(df, line_v)
+
+
+
+      if (c>chunk){
+        write_to_table(df, db_con, name, TRUE, filter_Score, filter_Rank)
+        c=0
+        df <- df_blanks
+
+      }
+      c = c+1
+
+      print(line)
+    }
+
+
+
+    close(con)
+
+
+}
+
+write_to_table <- function(df, db_con, name, append){
+
+       df <- df[!df$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$UID, '-', 3)
+        colnames(df_ids) <- c('grp_id', 'file_id', 'pid')
+        df <- cbind(df_ids, df)
+        DBI::dbWriteTable(db_con, name=name, value=df, row.names=FALSE, append=append)
+}
+
+add_probmetab <- function(pth, con){
+  if (!is.null(pth)){
+
+      df <- read.table(pth,  header = TRUE, sep='\t', stringsAsFactors = FALSE,  comment.char = "")
+      df$grp_id <- 1:nrow(df)
+      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$metfrag_result, con, filter_Score=0.6, filter_Rank=NA)
+add_extra_table_elucidation('sirius_csifingerid_results', opt$sirius_csifingerid_result, con, filter_Score=NA, filter_Rank=5)
+add_probmetab(opt$probmetab_result, con)
+
+
+
+
+cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
+             'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
+             'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ',
+             'FROM c_peak_groups AS cpg ',
+             'LEFT JOIN c_peak_X_c_peak_group AS cXg ON cXg.grpid=cpg.grpid ',
+             'LEFT JOIN c_peaks on c_peaks.cid=cXg.cid ',
+             'LEFT JOIN c_peak_X_s_peak_meta AS cXs ON cXs.cid=c_peaks.cid ',
+             'LEFT JOIN s_peak_meta ON cXs.pid=s_peak_meta.pid ',
+             'LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid')
+
+print(cmd)
+cpeakgroup_msms <- DBI::dbGetQuery(con, cmd)
+
+write.table(cpeakgroup_msms, file.path(opt$out_dir, 'cpeakgroup_msms.tsv'), row.names=FALSE, sep='\t')
--- a/create_sqlite_db.R	Thu May 31 09:08:55 2018 -0400
+++ b/create_sqlite_db.R	Thu May 31 11:23:09 2018 -0400
@@ -142,52 +142,18 @@
     if (is.null(pth)){
         return(0)
     }
-    index <- 0
-    chunkSize <- 5000
-    print(pth)
-    con <- file(description=pth,open="r")
-    df <- read.table(con, nrows=chunkSize,  header = TRUE, sep='\t', stringsAsFactors = FALSE,  comment.char = "")
-    headers = colnames(df)
-    print(head(df))
-    write_to_table(df, db_con, name, FALSE, filter_Score, filter_Rank)
+    DBI::dbWriteTable(conn=db_con, name=name, value=pth, sep='\t', header=T)

-    repeat {
-        index <- index + 1
-        print(paste('Processing rows:', index * chunkSize))
-
-        if (nrow(df) != chunkSize){
-                print('Processed all files!')
-                break
-        }
-
-        df <- read.table(con, nrows=chunkSize, skip=0, header = FALSE, sep='\t', stringsAsFactors = FALSE,  comment.char = "")
-        colnames(df) <- headers
-
-
-	write_to_table(df, db_con, name, TRUE, filter_Score, filter_Rank)
-
-
-        break
-    }
-   close(con)

 }

-write_to_table <- function(df, db_con, name, append, filter_Score, filter_Rank){
+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')

-        if (!is.na(filter_Score)){
-           df <- df[df$Score>=filter_Score,]
-        }
-
-        if (!is.na(filter_Rank)){
-
-            df <- df[df$Rank<=filter_Rank,]
-        }

         # get peakid, an scan id
         df_ids <- stringr::str_split_fixed(df$UID, '-', 3)
@@ -243,8 +209,13 @@
 add_extra_table_elucidation('sirius_csifingerid_results', opt$sirius_csifingerid_result, con, filter_Score=NA, filter_Rank=5)
 add_probmetab(opt$probmetab_result, con)

+if (is.null(xset)){
+  DBI::dbWriteTable(con, name='xset_classes', value=xa@xcmsSet@phenoData, row.names=TRUE)
+}else{

+  DBI::dbWriteTable(con, name='xset_classes', value=xset@phenoData, row.names=TRUE)

+}

 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, ',