R/IO.fun.R

In gecko515/HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs

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## IO FUNCTIONS ##
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#' @title Parse an HPO OBO file
#' @description Read an HPO OBO file (\href{http://human-phenotype-ontology.github.io/}{HPO}) and write 
#' the edges of the DAG on a plain text file. The format of the file is a sequence of
#' rows and each row corresponds to an edge represented through a pair of vertices separated by blanks.
#' @details a faster and more flexible parser to handle \emph{obo} file can be found \href{https://github.com/marconotaro/obogaf-parser}{here}.
#' @param obofile an HPO OBO file. The extension of the obofile can be or plain format (".txt") or compressed (".gz").
#' @param file name of the file of the edges to be written.
#' The extension of the file can be or plain format (".txt") or compressed (".gz").
#' @return a text file representing the edges in the format: source  destination (i.e. one row for each edge). 
#' @export
#' @examples
#' \dontrun{
#' hpobo <- "http://purl.obolibrary.org/obo/hp.obo";
#' do.edges.from.HPO.obo(obofile=hpobo, file="hp.edge");}
do.edges.from.HPO.obo <- function(obofile="hp.obo", file="edge.file"){
    tmp <- strsplit(obofile, "[.,/,_]")[[1]];
    if(any(tmp %in% "gz")){
        con <- gzfile(obofile);
        line <- readLines(con);    
        close(con);        
    }else{
        line <- readLines(obofile);
    }
    n.lines <- length(line);
    m <- matrix(character(1000000*2), ncol=2);
    colnames(m) <- c("source", "destination");
    i <- 1;
    j <- 0; # number of edges;
    while(i<=n.lines){
        while((i<=n.lines) && (line[i]!="[Term]")){
            i <- i + 1;
        }
        if(i>=n.lines){break();}
        i <- i + 1; # id
        destination <- strsplit(line[i], split="[ +\t]")[[1]][2];
        while( (line[i]!="") && (strsplit(line[i], split="[ +\t]")[[1]][1]!="is_a:") ){ # checking first is_a entry
            i <- i + 1;
        }
        if (line[i] == ""){next();}  # we are at the end of the record and is_a has been found
        source <- strsplit(line[i], split="[ +\t]")[[1]][2];
        j <- j + 1;
        i <- i + 1;
        m[j,]<-c(source,destination);
        while( (line[i]!="") && (strsplit(line[i], split="[ +\t]")[[1]][1]=="is_a:") ){# checking successive is_a entry
            source <- strsplit(line[i], split="[ +\t]")[[1]][2];
            i <- i + 1;
            j <- j + 1;
            m[j,]<-c(source,destination);
        }
    }
    m <- m[1:j,];
    tmp <- strsplit(file, "[.,/,_]")[[1]];
    if(any(tmp %in% "gz")){
        write.table(m, file=gzfile(file), quote=FALSE, row.names=FALSE, col.names=FALSE);
    }else{
        write.table(m, file=file, quote=FALSE, row.names=FALSE, col.names=FALSE);
    }
}

#' @title Write a directed graph on file
#' @description An object of class \code{graphNEL} is read and the graph is written on a plain text file as sequence of rows. 
#' @param g a graph of class \code{graphNEL}.
#' @param file name of the file to be written. The extension of the file can be or plain format (".txt") or compressed (".gz").
#' @return a plain text file representing the graph. Each row corresponds to an edge represented through a pair of vertices separated by blanks.
#' @export
#' @examples
#' data(graph);
#' tmpdir <- paste0(tempdir(),"/");
#' file <- paste0(tmpdir,"graph.edges.txt.gz");
#' write.graph(g, file=file);
write.graph <- function(g, file="graph.txt.gz"){  
    num.edges <- length(unlist(edges(g)));
    num.v <- numNodes(g);
    m <- matrix(character(num.edges*2), ncol=2);
    res <- edges(g);
    count=0;
    node1 <- names(res);
    for (i in 1:num.v) {
        x <- res[[i]];
    len.x <- length(x);
    if (len.x!=0)
        for (j in 1:len.x) {
            count <- count + 1;
            m[count,] <- c(node1[i],x[j]);
        }
    }
    tmp <- strsplit(file, "[.,/,_]")[[1]];
    if(any(tmp %in% "gz")){
        write.table(m, file=gzfile(file), quote=FALSE, row.names=FALSE, col.names=FALSE);
    }else{
        write.table(m, file=file, quote=FALSE, row.names=FALSE, col.names=FALSE);
    }
}

#' @title Read a directed graph from a file
#' @description A directed graph is read from a file and a \code{graphNEL} object is built.
#' @param file name of the file to be read. The format of the file is a sequence of rows and each row corresponds 
#' to an edge represented through a pair of vertices separated by blanks. 
#' The extension of the file can be or plain format (".txt") or compressed (".gz").
#' @return an object of class \code{graphNEL}.
#' @export
#' @examples
#' ed <- system.file("extdata/graph.edges.txt.gz", package= "HEMDAG");
#' g <- read.graph(file=ed);
read.graph <- function(file="graph.txt.gz"){ 
    tmp <- strsplit(file, "[.,/,_]")[[1]];
    if(any(tmp %in% "gz")){
        m <- as.matrix(read.table(gzfile(file), colClasses="character"));
    }else{
        m <- as.matrix(read.table(file, colClasses="character"));
    }
    thenodes<-sort(unique(as.vector(m))); # nodes
    n.nodes <- length(thenodes);
    n.edges <- nrow(m);
    # building the graph
    edL <- vector("list", length=n.nodes);
    names(edL) <- thenodes;
    for(i in 1:n.nodes)
        edL[[i]]<-list(edges=NULL);
    g <- graphNEL(nodes=thenodes, edgeL=edL, edgemode="directed");
    g <- addEdge(m[1:n.edges,1], m[1:n.edges,2], g, rep(1,n.edges));
    return(g);
}

#' @title Read an undirected graph from a file
#' @description The graph is read from a file and a \code{graphNEL} object is built. The format of the input file is a sequence of rows. 
#' Each row corresponds to an edge represented through a pair of vertices separated by blanks, and the weight of the edge.
#' @param file name of the file to be read. The extension of the file can be or plain format (".txt") or compressed (".gz").
#' @return a graph of class \code{graphNEL}.
#' @export
#' @examples
#' edges <- system.file("extdata/edges.txt.gz", package="HEMDAG");
#' g <- read.undirected.graph(file=edges);
read.undirected.graph <- function(file="graph.txt.gz") {  
    tmp <- strsplit(file, "[.,/,_]")[[1]];
    if(any(tmp %in% "gz")){
        m <- as.matrix(read.table(gzfile(file), colClasses="character"));
    }else{
        m <- as.matrix(read.table(file, colClasses="character"));
    }
    thenodes<-sort(unique(as.vector(m[,1:2]))); # nodes
    n.nodes <- length(thenodes);
    n.edges <- nrow(m);
    # building the graph
    edL <- vector("list", length=n.nodes);
    names(edL) <- thenodes;
    for(i in 1:n.nodes)
        edL[[i]]<-list(edges=NULL);
    g <- graphNEL(nodes=thenodes, edgeL=edL, edgemode="undirected");
    g <- addEdge(m[1:n.edges,1], m[1:n.edges,2], g, as.numeric(m[1:n.edges,3]));
    return(g);
}