R/io.R

In korsunskylab/gagarin: (spat)ial genomics analysis (t)ools (ula)

## Useful functions for reading and writing files 


#' @export 
writeMM <- function(X, fname) {
    stopifnot(is(X, 'dgCMatrix'))
    nelem <- length(X@i)
    nrow <- X@Dim[1]
    ncol <- X@Dim[2]    
    writeLines(paste0(c('%%MatrixMarket matrix coordinate real general\n', nrow, ' ', ncol, ' ', nelem), collapse = ''), fname)    
    fwrite(data.table(X@i+1, rep(seq_len(ncol), times = diff(X@p)), X@x), fname, append = TRUE, sep = ' ')        
}

#' @export 
readMM <- function(fname, max_header_size = 100, nthreads = NULL) {
    ## First, figure out how many lines to skip
    ## Assumes that MM format has comments that start with %
    nlines_skip <- 0
    con <- file(fname, open = 'r')
    for (i in seq_len(max_header_size)) {
        line <- readLines(con, 1)
        nlines_skip <- nlines_skip + 1
        if (!grepl('^\\W*\\%', line)) {
            ## This is the line with dimension information 
            ## We need dimension information to handle empty rows and columns 
            nrow <- as.integer(strsplit(line, ' ')[[1]][1])
            ncol <- as.integer(strsplit(line, ' ')[[1]][2])
            break
        }
    }
    close(con)

    if (is.null(nthreads)) {
        nthreads <- data.table::getDTthreads()
    }
    ## Then, read the file and make a matrix 
    with(
        fread(fname, skip = nlines_skip, nThread = nthreads),
        Matrix::sparseMatrix(i = V1, j = V2, x = V3, dims = c(nrow, ncol))
    )
}