R/KEGG.annotationvold.R

In yufree/xMSannotator: xMSannotator: R package for network based annotation of metabolomics data.

#' KEGG.Gene.ID',
#' 
#' KEGG.Gene.ID',
#' 
#' 
KEGG.annotationvold <- function(dataA, max.mz.diff = 10, 
    queryadductlist = c("M+H"), xMSannotator.outloc, numnodes = 1, 
    syssleep = 1, adduct_table) {
    data_a <- as.data.frame(dataA)
    
    # print('Using the 1st column as \'mz\' for
    # annotation.')
    
    mzlist <- data_a[, 1]
    
    dir.create(xMSannotator.outloc, showWarnings = FALSE)
    setwd(xMSannotator.outloc)
    
    # adduct_table<-read.table('/Users/karanuppal/Documents/Emory/JonesLab/Projects/xMSannotator/adduct_table.txt',sep='\t',header=TRUE)
    # adduct_table<-adduct_table[c(which(adduct_table[,6]=='S'),which(adduct_table[,6]=='Acetonitrile')),]
    
    adduct_names <- as.character(adduct_table[, 1])
    adductlist <- adduct_table[, 4]
    mult_charge <- adduct_table[, 3]
    num_mol <- adduct_table[, 2]
    names(adductlist) <- as.character(adduct_names)
    names(mult_charge) <- as.character(adduct_names)
    names(num_mol) <- as.character(adduct_names)
    alladducts <- adduct_names
    
    if (queryadductlist[1] == "positive") {
        queryadductlist <- adduct_names[which(adduct_table[, 
            5] == "positive")]
        
    } else {
        if (queryadductlist[1] == "negative") {
            
            queryadductlist <- adduct_names[which(adduct_table[, 
                5] == "negative")]
            
        } else {
            if (queryadductlist[1] == "all") {
                
                
                queryadductlist <- alladducts
                
                
            } else {
                if (length(which(queryadductlist %in% alladducts == 
                  FALSE)) > 0) {
                  
                  errormsg <- paste("Adduct should be one of:", 
                    sep = "")
                  for (i in alladducts) {
                    errormsg <- paste(errormsg, i, sep = " ; ")
                  }
                  stop(errormsg, "\n\nUsage: feat.batch.annotation.KEGG(dataA,max.mz.diff=10, queryadductlist=c(\"M+H\", \"M+Na\"), xMSannotator.outloc, numnodes=1)", 
                    "\n\n OR  feat.batch.annotation.KEGG(dataA,max.mz.diff=10, queryadductlist=c(\"positive\"), xMSannotator.outloc, numnodes=1)", 
                    "\n\n OR  feat.batch.annotation.KEGG(dataA,max.mz.diff=10, queryadductlist=c(\"negative\"), xMSannotator.outloc, numnodes=1)", 
                    "\n\n OR  feat.batch.annotation.KEGG(dataA,max.mz.diff=10, queryadductlist=c(\"all\"), xMSannotator.outloc, numnodes=1)")
                }
                
            }
        }
    }
    
    parentres = {
    }
    # cnames<-c('','Adduct','Query.m/z', 'Search mass \n
    # tolerance range (+/-)', 'Metlin', 'Compound.Name',
    # 'CASID', 'KEGG.Compound.ID', 'KEGG.Pathway.name',
    # 'KEGG.Pathway.ID', 'HMDB.ID', 'PubChem.Substance.ID',
    # 'PubChem.Compound.ID', 'ChEBI.ID', 'LIPID.MAPS.ID')
    cnames <- c("", "Adduct", "Query.m/z", "Search mass \n tolerance range (+/-)", 
        "Metlin", "Compound.Name", "Chemical.Formula", "Exact Mass", 
        "CASID", "KEGG.Compound.ID", "KEGG.Pathway.ID", "KEGG.Pathway.name", 
        "HMDB.ID", "PubChem.Substance.ID", "ChEBI.ID", "LIPID.MAPS.ID", 
        "KEGG.Brite.Category", "KEGG.Disease.ID", "KEGG.Drug.ID", 
        "KEGG.Environ.ID")
    
    
    for (adnum in 1:length(queryadductlist)) {
        adductname = queryadductlist[adnum]
        adductmass = adductlist[as.character(adductname)]
        
        cl <- makeSOCKcluster(numnodes)
        
        clusterEvalQ(cl, library(XML))
        clusterEvalQ(cl, library(RCurl))
        clusterEvalQ(cl, "feat.batch.annotation.child")
        
        # print(paste('Query adduct: ',adductname,sep=''))
        
        mz.annot.res <- new("list")
        min_mz <- min(mzlist)
        max_mz <- max(mzlist)
        
        mz_group <- ceiling(max_mz/min_mz)
        
        # mz_group<-round(max_mz/10) length(mzlist)
        num_mz <- 1
        
        for (mind in seq(1, length(mzlist), mz_group)) {
            
            stopind <- mind + mz_group
            if (stopind > length(mzlist)) {
                
                stopind <- length(mzlist)
            }
            s1 <- mzlist[mind:stopind]
            s1 <- unique(s1)
            num_mz <- num_mz + length(s1)
            
            if (num_mz%%50 > 0) {
                Sys.sleep((syssleep/2))
            } else {
                Sys.sleep(syssleep)
            }
            if (length(s1) > 1) {
                
                mz.annot.res <- c(mz.annot.res, parLapply(cl, 
                  s1, feat.batch.annotation.child, max.mz.diff = max.mz.diff, 
                  adductname = adductname, adduct_table = adduct_table, 
                  syssleep = syssleep))
                
            } else {
                for (i in 1:length(s1)) {
                  rescur <- feat.batch.annotation.child(mz.val = s1[i], 
                    max.mz.diff = max.mz.diff, adductname = adductname, 
                    adduct_table = adduct_table, syssleep = syssleep)
                  # print(length(rescur))
                  if (length(rescur) > 0) {
                    rescur <- as.matrix(rescur)
                    # print(dim(rescur))
                    if (dim(rescur)[2] == 1) {
                      rescur <- t(rescur)
                      rescur <- as.data.frame(rescur)
                    }
                    rescur <- as.data.frame(rescur)
                    # print(dim(rescur))
                    mz.annot.res <- c(mz.annot.res, rescur)
                  }
                }
            }
            if (mind%%10 > 0) {
                Sys.sleep((syssleep/10))
            } else {
                Sys.sleep(syssleep)
                stopCluster(cl)
                cl <- makeSOCKcluster(numnodes)
                
                
                clusterEvalQ(cl, library(XML))
                clusterEvalQ(cl, library(RCurl))
                clusterEvalQ(cl, "feat.batch.annotation.child")
            }
            
        }
        
        stopCluster(cl)
        res = {
        }
        # print(adductname)
        if (length(mz.annot.res) > 0) {
            for (mzl in 1:length(mz.annot.res)) {
                res = rbind(res, mz.annot.res[[mzl]])
                
            }
        }
        res <- unique(res)
        
        text_res <- {
        }
        
        if (length(res) > 0) {
            
            adductname = c(rep(adductname, dim(res)[1]))
            
            temp_res <- cbind(adductname, res)
            
            temp_res <- as.matrix(temp_res)
            
            
            
            if (dim(temp_res)[2] == 1) {
                
                temp_res <- t(temp_res)
                temp_res <- as.data.frame(temp_res)
                
            }
            
            bad_rows <- which(temp_res[, 2] == "1")
            
            if (length(bad_rows) > 0) {
                temp_res <- temp_res[-bad_rows, ]
                temp_res <- as.matrix(temp_res)
                
                # temp_res<-t(temp_res)
                if (dim(temp_res)[2] == 1) {
                  
                  temp_res <- t(temp_res)
                  
                  
                }
                
                
            }
            # temp_res<-as.data.frame(temp_res)
            colnames(temp_res) = NULL
            
            
            # text_resindex<-c(1,2,5,6,7,8,11,10,13,15,17,19,21)
            # text_resindex<-c(1,2,5,6,7,8,9,12,11,14,16,18,20,22)
            
            # text_resindex<-c(1,2,5,6:8,9,11,13,14,16,18,20,21)
            # text_resindex<-c(1,2,5,6:7,4,8,10,12,13,17,19,21)
            
            text_resindex <- c(1, 2, 5, 6:7, 4, 8, 9, 11, 
                13, 14, 16, 18, 20, 22, 26:28)
            text_resindex <- text_resindex + 1
            # print(dim(temp_res))
            text_res <- temp_res[, c(1, text_resindex)]
            
            text_res <- as.matrix(text_res)
            
            if (dim(text_res)[2] == 1) {
                
                text_res <- t(text_res)
                
                
            }
            text_res <- as.data.frame(text_res)
            bad_rows <- which(text_res[, 2] == "1")
            
            
            if (length(bad_rows) > 0) {
                text_res <- text_res[-bad_rows, ]
                text_res <- as.matrix(text_res)
                text_res <- t(text_res)
            }
            text_res <- as.data.frame(text_res)
            
            sernum = seq(1, dim(text_res)[1])
            text_res <- cbind(sernum, text_res)
            colnames(text_res) = cnames
            text_res <- text_res[, -c(5)]
            
            parentres = rbind(parentres, temp_res)
            rm(temp_res)
            colnames(parentres) = NULL
            
        }
        # num_cols<-dim(text_res)[2]
        # text_res<-cbind(text_res[,c(1:10)],text_res[,c(num_cols)],text_res[,c(11:(num_cols-1))])
        fname = paste(xMSannotator.outloc, "/KEGG_annotation_results_", 
            queryadductlist[adnum], ".txt", sep = "")
        write.table(text_res, file = fname, sep = "\t", row.names = FALSE)
        
        
        
        Sys.sleep(syssleep)
        
    }
    
    html_res <- {
    }
    text_res <- {
    }
    
    
    if (length(parentres) > 0) {
        
        res <- parentres[order(parentres[, 2]), ]
        
        # html_resindex<-c(1,2,5,4,6:7,9,11:12,14,16,18,20,22)
        res <- as.matrix(res)
        
        if (dim(res)[2] == 1) {
            res <- t(res)
        }
        
        
        
        # html_resindex<-c(1,2,5,6:7,9,11:12,14,16,18,20,22)
        
        # html_resindex<-c(1,2,5,6:7,4,8,10,12,13,15,17,19,21)
        html_resindex <- c(1, 2, 5, 6:7, 4, 8, 10, 12, 13, 
            15, 17, 19, 21, 22, 23:25)
        
        html_resindex <- html_resindex + 1
        html_res <- res[, c(1, html_resindex)]
        html_res <- as.matrix(html_res)
        
        
        if (dim(html_res)[2] == 1) {
            html_res <- t(html_res)
        }
        
        sernum = seq(1, dim(html_res)[1])
        
        # html_res<-cbind(sernum,html_res)
        html_res <- as.data.frame(html_res)
        
        cnames <- c("Adduct", "Query.m/z", "Search mass \n tolerance range (+/-)", 
            "Metlin", "Compound.Name", "Chemical.Formula", 
            "Exact Mass", "CASID", "KEGG.Compound.ID", "KEGG.Pathway.ID", 
            "KEGG.Pathway.Name", "HMDB.ID", "PubChem.Substance.ID", 
            "ChEBI.ID", "LIPID.MAPS.ID", "KEGG.Brite.Category", 
            "KEGG.Disease.ID", "KEGG.Drug.ID", "KEGG.Environ.ID")
        
        #'KEGG.Gene.ID',
        
        colnames(html_res) <- cnames
        
        html_res <- html_res[, -c(4)]
        # fname=paste('Annotation_results',sep='')
        # num_cols<-dim(html_res)[2]
        # text_res<-cbind(html_res[,c(1:10)],html_res[,c(num_cols)],html_res[,c(11:(num_cols-1))])
        
        fname = paste("KEGG_annotation_results", sep = "")
        unlink(fname)
        # fname=paste(xMSannotator.outloc,'/KEGG_annotation_results.html',sep='')
        HTMLInitFile(filename = fname, Title = "KEGG annotation results", 
            outdir = xMSannotator.outloc)
        fname = paste(xMSannotator.outloc, "/KEGG_annotation_results.html", 
            sep = "")
        HTML(html_res, file = fname, Border = 1, innerBorder = 1, 
            useCSS = TRUE)
        HTMLEndFile(file = fname)
        
        
        
        cnames <- c("", "Adduct", "Query.m/z", "Search mass \n tolerance range (+/-)", 
            "Metlin", "Compound.Name", "Chemical.Formula", 
            "Exact Mass", "CASID", "KEGG.Compound.ID", "KEGG.Pathway.ID", 
            "KEGG.Pathway.Name", "HMDB.ID", "PubChem.Substance.ID", 
            "ChEBI.ID", "LIPID.MAPS.ID", "KEGG.Brite.Category", 
            "KEGG.Disease.ID", "KEGG.Drug.ID", "KEGG.Environ.ID")
        
        # text_resindex<-c(1,2,5,6:7,4,8,9,11,13,14,16,18,20,22)
        # #c(1,2,5,6,7,8,9,12,11,14,16,18,20,22)
        
        # text_resindex<-c(1,2,5,6:7,4,8,10,12,13,17,19,21)
        
        # text_resindex<-c(1,2,5,6:7,4,8,9,11,13,14,16,18,20,22,29:33)
        text_resindex <- c(1, 2, 5, 6:7, 4, 8, 9, 11, 13, 
            14, 16, 18, 20, 22, 26:28)
        text_resindex <- text_resindex + 1
        text_res <- res[, c(1, text_resindex)]
        
        text_res <- as.matrix(text_res)
        if (dim(text_res)[2] == 1) {
            text_res <- t(text_res)
        }
        
        if (length(text_res) > 0) {
            sernum = seq(1, dim(text_res)[1])
        } else {
            sernum = {
            }
        }
        text_res <- cbind(sernum, text_res)
        
        text_res <- as.data.frame(text_res)
        colnames(text_res) = cnames
        text_res <- text_res[, -c(5)]
        # num_cols<-dim(text_res)[2]
        # text_res<-cbind(text_res[,c(1:10)],text_res[,c(num_cols)],text_res[,c(11:(num_cols-1))])
        fname = paste(xMSannotator.outloc, "/KEGG_annotation_results_alladducts.txt", 
            sep = "")
        write.table(text_res, file = fname, sep = "\t", row.names = FALSE)
    }
    return(list(text.res = text_res, html.res = html_res))
}