R/readPaf.R

In daewoooo/SVbyEye: Visualization of genomic structural variants

#' Read PAF from an input file
#'
#' This function takes an PAF output file from minimap2 and loads the file along
#' with user defined set of additional alignment tags (see PAF specification).
#'
#' @param paf.file A path to a PAF file containing alignments to be loaded.
#' @param include.paf.tags Set to \code{TRUE} if all additional PAF alignment tags should be included in the output.
#' @param restrict.paf.tags Define a set of PAF tag ids (e.g. NM, cg) to be reported in the output.
#' @importFrom stringr str_split
#' @importFrom dplyr bind_cols
#' @importFrom S4Vectors lapply
#' @return A \code{tibble} of loaded PAF alignments
#' @author David Porubsky
#' @export
#' @examples
#' ## Get PAF to read in ##
#' paf.file <- system.file("extdata", "test1.paf", package = "SVbyEye")
#' ## Read in PAF
#' paf.table <- readPaf(paf.file = paf.file)
#' ## Read in PAF including all tags
#' paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE)
#' ## Read in PAF including CIGAR string only
#' paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
#'
readPaf <- function(paf.file = NULL, include.paf.tags = TRUE, restrict.paf.tags = c("NM", "cg")) {
    ## Check user input ##
    if (is.null(paf.file)) {
        stop("Path to a PAF file to load is not defined!!!")
    }

    ## Check if file exists and is TAB delimited
    if (file.exists(paf.file)) {
        con <- file(paf.file, "r")
        first.line <- readLines(con, n = 1)
        n.fields <- length(stringr::str_split(first.line, "\t")[[1]])
        if (n.fields < 12) {
            stop("User defined 'paf.file' has less then 12 expected tab-delimeted fields!!!")
        }
        close(con)
    } else {
        stop("User defined 'paf.file' doesn't exist!!!")
    }

    ## Load PAF file ##
    if (file.exists(paf.file)) {
        ptm <- startTimedMessage(paste0("[readPaf] Loading PAF file: ", paf.file))
        ## Read PAF lines
        paf.lines <- readLines(paf.file)
        if (include.paf.tags) {
            fields <- stringr::str_split(paf.lines, "\t")
        } else {
            fields <- stringr::str_split(paf.lines, "\t", 13)
        }
        paf.fields <- S4Vectors::lapply(fields, "[", seq_len(12))
        field.names <- c("q.name", "q.len", "q.start", "q.end", "strand", "t.name", "t.len", "t.start", "t.end", "n.match", "aln.len", "mapq")

        for (i in seq_along(paf.fields)) {
            attr(paf.fields[[i]], "names") <- field.names
        }
        paf <- dplyr::bind_rows(paf.fields)
        cols.num <- c(2, 3, 4, 7:12)
        paf[cols.num] <- suppressWarnings(dplyr::bind_cols(S4Vectors::lapply(paf[cols.num], as.numeric)))

        if (include.paf.tags) {
            if (any(lengths(fields) > 12)) {
                paf.tags <- S4Vectors::lapply(fields, function(x) paste(x[13:length(x)]))
                paf <- dplyr::bind_cols(paf, processPafTags(paf.tags = paf.tags, restrict.paf.tags = restrict.paf.tags))
            }
        }
        stopTimedMessage(ptm)
        return(paf)
    } else {
        stop(paste0("PAF file ", paf.file, " doesn't exists !!!"))
        return(NULL)
    }
}

#' Process PAF specific alignment tags.
#'
#' @param paf.tags A \code{list} of PAF specific tag extracted from each alignment.
#' @inheritParams readPaf
#' @importFrom stringr str_split
#' @importFrom dplyr bind_rows
#' @return A \code{tibble} object
#' @author David Porubsky
#'
processPafTags <- function(paf.tags, restrict.paf.tags = c("NM", "cg")) {
    ## Make sure restrict.paf.tags takes only expected values
    allowed.tags <- c("tp", "cm", "s1", "s2", "NM", "MD", "AS", "SA", "ms", "nn", "ts", "cg", "cs", "dv", "de", "rl")
    restrict.paf.tags <- restrict.paf.tags[restrict.paf.tags %in% allowed.tags]
    if (length(restrict.paf.tags) == 0) {
        message(paste0("Submitted 'restrict.paf.tags' are not present in the allowed set of PAF tags: ", paste(allowed.tags, collapse = "; ")))
        restrict.paf.tags <- NULL
    }

    tags <- character()
    to.numeric <- integer()
    res <- list()
    n <- length(paf.tags)
    t.idx <- 0
    for (ali.idx in seq_along(paf.tags)) {
        split.tags <- stringr::str_split(paf.tags[[ali.idx]], ":")
        for (tag in split.tags) {
            if (!is.null(restrict.paf.tags) & tag[1] %in% restrict.paf.tags) {
                if (!(tag[1] %in% tags)) {
                    t.idx <- t.idx + 1
                    if (tag[2] %in% c("f", "H", "i")) {
                        to.numeric <- c(to.numeric, t.idx)
                    }
                    res[[tag[1]]] <- rep(NA, n)
                    tags <- c(tags, tag[1])
                }
                res[[tag[1]]][ali.idx] <- tag[3]
            }
        }
    }

    for (i in to.numeric) {
        res[[i]] <- as.numeric(res[[i]])
    }
    dplyr::bind_rows(res)
}