R/rbh2dagchainer.R
In kullrich/CRBHits: Conditional reciprocal best hits (CRBHits) in R
Defines functions
rbh2dagchainer
Documented in
rbh2dagchainer
#' @title rbh2dagchainer
#' @name rbh2dagchainer
#' @description This function runs DAGchainer
#' (http://dagchainer.sourceforge.net/) given CRBHit pairs and gene positions
#' for both cds1 and cds2. The default options are set to not compare gene
#' positions in base pairs but instead using gene order (gene.idx).
#' @param rbhpairs (conditional-)reciprocal best hit (CRBHit) pair result
#' (see \code{\link[CRBHits]{cds2rbh}}) [mandatory]
#' @param selfblast1 (conditional-)reciprocal best hit (CRBHit) pair selfblast
#' result for cds1 sequences (see \code{\link[CRBHits]{cds2rbh}}) [optional]
#' @param selfblast2 (conditional-)reciprocal best hit (CRBHit) pair selfblast
#' result for cds2 sequences (see \code{\link[CRBHits]{cds2rbh}}) [optional]
#' @param gene.position.cds1 specify gene position for cds1 sequences
#' (see \code{\link[CRBHits]{cds2genepos}}) [default: NULL]
#' @param gene.position.cds2 specify gene position for cds2 sequences
#' (see \code{\link[CRBHits]{cds2genepos}}) [default: NULL]
#' @param dagchainerpath specify the PATH to the DAGchainer binaries
#' [default: /extdata/dagchainer/]
#' @param gap_open_penalty gap open penalty [default: 0]
#' @param gap_extension_penalty gap extension penalty [default: -3]
#' @param gap_length length of a gap (avgerage distance expected between two
#' syntenic genes); if type is set to "idx" use 1 [default: 10000]
#' @param max_match_score Maximum match score [default: 50]
#' @param max_dist_allowed maximum distance allowed between two matches;
#' if type is set to "idx" use 20 [default: 200000]
#' @param max_evalue Maximum E-value [default: 1e-3]
#' @param ignore_tandem ignore tandem duplicates [default = TRUE]
#' @param only_tandem only tandem alignments [default = FALSE]
#' @param min_number_aligned_pairs Minimum number of Aligned Pairs [default: 5]
#' @param type specify if gene order index "idx" or gene base pair position
#' "bp" should be extracted and used with DAGchainer [default: bp]
#' @param plotDotPlot specify if dotplot should be plotted [default: FALSE]
#' @param DotPlotTitle specify DotPlot title [default: 'DAGchainer results']
#' @param colorBy specify if dagchainer groups should be colored by "Ka", "Ks",
#' "Ka/Ks" or "none" [default: none]
#' @param kaks specify Ka/Ks input obtained via `rbh2kaks()` [default: NULL]
#' @param ka.max specify max Ka to be filtered [default: 5]
#' @param ks.max specify max Ks to be filtered [default: 5]
#' @param ka.min specify min Ka to be filtered [default: 0]
#' @param ks.min specify min Ks to be filtered [default: 0]
#' @param select.chr filter results for chromosome names [default: NULL]
#' @return \code{DAGchanier} results\cr
#' 1: $gene1.chr\cr
#' 2: $gene1.seq.id\cr
#' 3: $gene1.start\cr
#' 4: $gene1.end\cr
#' 5: $gene1.mid\cr
#' 6: $gene1.idx\cr
#' 7: $gene2.chr\cr
#' 8: $gene2.seq.id\cr
#' 9: $gene2.start\cr
#' 10: $gene2.end\cr
#' 11: $gene2.mid\cr
#' 12: $gene2.idx\cr
#' 13: $evalue\cr
#' 14: $score\cr
#' @importFrom tidyr %>%
#' @importFrom dplyr bind_cols select group_by group_map group_keys mutate
#' @importFrom stringr word
#' @importFrom ggplot2 ggplot geom_point geom_abline facet_wrap
#' @importFrom utils write.table
#' @seealso \code{\link[CRBHits]{plot_dagchainer}},
#' \code{\link[CRBHits]{cds2genepos}},
#' \code{\link[CRBHits]{tandemdups}},
#' \code{\link[CRBHits]{rbh2kaks}}
#' @references Haas BJ et al. (2004) DAGchainer: a tool for mining segmental
#' genome duplications and synteny. \emph{Bioinformatics.}
#' \bold{20(18)}, 3643-3646.
#' @examples
#' ## compile dagchainer
#' CRBHits::make_dagchainer()
#' ## load example sequence data
#' data("ath", package="CRBHits")
#' ## get selfhits CRBHit pairs
#' ath_selfhits_crbh <- cds2rbh(
#' cds1=ath,
#' cds2=ath,
#' plotCurve=TRUE)
#' ## get gene position
#' ath.genepos <- cds2genepos(
#' cds=ath,
#' source="ENSEMBL")
#' ## get DAGchainer results
#' ath_selfblast_crbh.dagchainer <- rbh2dagchainer(
#' rbhpairs=ath_selfhits_crbh,
#' gene.position.cds1=ath.genepos,
#' gene.position.cds2=ath.genepos)
#' head(ath_selfblast_crbh.dagchainer)
#' ## plot dagchainer
#' plot_dagchainer(
#' dag=ath_selfblast_crbh.dagchainer)
#' @export rbh2dagchainer
#' @author Kristian K Ullrich
rbh2dagchainer <- function(rbhpairs,
selfblast1=NULL,
selfblast2=NULL,
gene.position.cds1=NULL,
gene.position.cds2=NULL,
dagchainerpath=paste0(find.package("CRBHits"),
"/extdata/dagchainer/"),
gap_open_penalty=0,
gap_extension_penalty=-3,
gap_length=10000,
max_match_score=50,
max_dist_allowed=200000,
max_evalue=1e-3,
ignore_tandem=TRUE,
only_tandem=FALSE,
min_number_aligned_pairs=5,
type="bp",
plotDotPlot=FALSE,
DotPlotTitle="DAGchainer results",
colorBy="none",
kaks=NULL,
ka.max=5,
ks.max=5,
ka.min=0,
ks.min=0,
select.chr=NULL
){
gene.seq.id <- NULL
gene1.seq.id <- NULL
gene2.seq.id <- NULL
gene.chr <- NULL
gene1.chr <- NULL
gene2.chr <- NULL
gene.start <- NULL
gene.end <- NULL
gene.idx <- NULL
gene1.idx1 <- NULL
gene1.idx2 <- NULL
gene2.idx1 <- NULL
gene2.idx2 <- NULL
evalue <- NULL
score <- NULL
if(ignore_tandem == TRUE & only_tandem == TRUE){
stop("both options set to TRUE can not go together. Set one of them to
FALSE")
}
if(attributes(rbhpairs)$CRBHits.class != "crbh"){
stop("Please obtain rbhpairs via the cds2rbh or the cdsfile2rbh
function")
}
if(is.null(gene.position.cds1) | is.null(gene.position.cds2)){
stop("Please provide gene position information. Can be obtained via the
cds2genepos() function")
}
if(!is.null(gene.position.cds1)){
if(attributes(gene.position.cds1)$CRBHits.class != "genepos"){
stop("Please obtain gene position via the cds2genepos() function or
add a 'genepos' class attribute")
}
}
if(!is.null(gene.position.cds2)){
if(attributes(gene.position.cds2)$CRBHits.class != "genepos"){
stop("Please obtain gene position via the cds2genepos() function or
add a 'genepos' class attribute")
}
}
if(!dir.exists(dagchainerpath)){
stop("Error: DAGchainer PATH does not exist. Please specify correct
PATH and/or look into package installation prerequisites. Try to
use make_dagchainer() function.")
}
if(!file.exists(paste0(dagchainerpath, "dagchainer"))){
stop("Error: dagchainer binary does not exist. Please specify correct
PATH and/or look into package installation prerequisites. Try to
use make_dagchainer() function.")
}
if(!file.exists(paste0(dagchainerpath, "run_DAG_chainer.pl"))){
stop("Error: run_DAG_chainer.pl does not exist. Please specify correct
PATH and/or look into package installation prerequisites. Try to use
make_dagchainer() function.")
}
selfblast <- attributes(rbhpairs)$selfblast
genepos.colnames <- c("gene.seq.id", "gene.chr", "gene.start", "gene.end",
"gene.mid", "gene.strand", "gene.idx")
if(plotDotPlot){
if(colorBy == "Ka" | colorBy == "Ks" | colorBy == "Ka/Ks"){
if(is.null(kaks)){
stop("Please provide Ka/Ks input as obtained via rbh2kaks()")
}
if(!is.null(kaks)){
if(attributes(kaks)$CRBHits.class != "kaks"){
stop("Please obtain Ka/Ks input via the rbh2kaks() function
or add a 'kaks' class attribute")
}
}
}
}
if(type=="bp"){
aa1.genepos <- gene.position.cds1[match(rbhpairs$crbh.pairs$aa1,
gene.position.cds1$gene.seq.id), , drop =FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
aa2.genepos <- gene.position.cds2[match(rbhpairs$crbh.pairs$aa2,
gene.position.cds2$gene.seq.id), , drop =FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
dagchainer.input <- cbind(aa1.genepos, aa2.genepos)
colnames(dagchainer.input) <- c("gene1.chr", "gene1.seq.id",
"gene1.start", "gene1.end", "gene2.chr", "gene2.seq.id",
"gene2.start", "gene2.end")
dagchainer.evalue <- rbhpairs$crbh1[match(dagchainer.input$gene1.seq.id,
rbhpairs$crbh1$query_id), , drop=FALSE]$evalue
dagchainer.input <- cbind(dagchainer.input, evalue=dagchainer.evalue)
if(selfblast){
dagchainer.input$gene1.chr<-paste0("AA1:",
dagchainer.input$gene1.chr)
dagchainer.input$gene2.chr<-paste0("AA1:",
dagchainer.input$gene2.chr)
} else{
dagchainer.input$gene1.chr<-paste0("AA1:",
dagchainer.input$gene1.chr)
dagchainer.input$gene2.chr<-paste0("AA2:",
dagchainer.input$gene2.chr)
}
if(!is.null(selfblast1)){
selfblast1.aa1.genepos <- gene.position.cds1[
match(selfblast1$crbh.pairs$aa1,
gene.position.cds1$gene.seq.id), , drop =FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
selfblast1.aa2.genepos <- gene.position.cds1[
match(selfblast1$crbh.pairs$aa2,
gene.position.cds1$gene.seq.id), , drop =FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
selfblast1.dagchainer.input <- cbind(selfblast1.aa1.genepos,
selfblast1.aa2.genepos)
colnames(selfblast1.dagchainer.input) <- c("gene1.chr",
"gene1.seq.id", "gene1.start", "gene1.end", "gene2.chr",
"gene2.seq.id", "gene2.start", "gene2.end")
selfblast1.dagchainer.evalue <- selfblast1$crbh1[
match(selfblast1.dagchainer.input$gene1.seq.id,
selfblast1$crbh1$query_id), , drop=FALSE]$evalue
selfblast1.dagchainer.input <- cbind(selfblast1.dagchainer.input,
evalue=selfblast1.dagchainer.evalue)
selfblast1.dagchainer.input$gene1.chr<-paste0("AA1:",
selfblast1.dagchainer.input$gene1.chr)
selfblast1.dagchainer.input$gene2.chr<-paste0("AA1:",
selfblast1.dagchainer.input$gene2.chr)
dagchainer.input <- rbind(dagchainer.input,
selfblast1.dagchainer.input)
}
if(!is.null(selfblast2)){
selfblast2.aa1.genepos <- gene.position.cds2[
match(selfblast2$crbh.pairs$aa1,
gene.position.cds2$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
selfblast2.aa2.genepos <- gene.position.cds2[
match(selfblast2$crbh.pairs$aa2,
gene.position.cds2$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
selfblast2.dagchainer.input <- cbind(selfblast2.aa1.genepos,
selfblast2.aa2.genepos)
colnames(selfblast2.dagchainer.input) <- c("gene1.chr",
"gene1.seq.id", "gene1.start", "gene1.end", "gene2.chr",
"gene2.seq.id", "gene2.start", "gene2.end")
selfblast2.dagchainer.evalue <- selfblast2$crbh1[
match(selfblast2.dagchainer.input$gene1.seq.id,
selfblast2$crbh1$query_id), , drop=FALSE]$evalue
selfblast2.dagchainer.input <- cbind(selfblast2.dagchainer.input,
evalue=selfblast2.dagchainer.evalue)
selfblast2.dagchainer.input$gene1.chr<-paste0("AA2:",
selfblast2.dagchainer.input$gene1.chr)
selfblast2.dagchainer.input$gene2.chr<-paste0("AA2:",
selfblast2.dagchainer.input$gene2.chr)
dagchainer.input <- rbind(dagchainer.input,
selfblast2.dagchainer.input)
}
}
if(type=="idx"){
aa1.genepos <- gene.position.cds1[match(rbhpairs$crbh.pairs$aa1,
gene.position.cds1$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
aa2.genepos <- gene.position.cds2[match(rbhpairs$crbh.pairs$aa2,
gene.position.cds2$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
dagchainer.input <- cbind(aa1.genepos, aa2.genepos)
colnames(dagchainer.input) <- c("gene1.chr", "gene1.seq.id",
"gene1.idx1", "gene1.idx2", "gene2.chr", "gene2.seq.id",
"gene2.idx1", "gene2.idx2")
dagchainer.evalue <- rbhpairs$crbh1[match(dagchainer.input$gene1.seq.id,
rbhpairs$crbh1$query_id), , drop=FALSE]$evalue
dagchainer.input <- cbind(dagchainer.input, evalue=dagchainer.evalue)
if(selfblast){
dagchainer.input$gene1.chr<-paste0("AA1:",
dagchainer.input$gene1.chr)
dagchainer.input$gene2.chr<-paste0("AA1:",
dagchainer.input$gene2.chr)
} else{
dagchainer.input$gene1.chr<-paste0("AA1:",
dagchainer.input$gene1.chr)
dagchainer.input$gene2.chr<-paste0("AA2:",
dagchainer.input$gene2.chr)
}
if(!is.null(selfblast1)){
selfblast1.aa1.genepos <- gene.position.cds1[
match(selfblast1$crbh.pairs$aa1,
gene.position.cds1$gene.seq.id), , drop =FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
selfblast1.aa2.genepos <- gene.position.cds1[
match(selfblast1$crbh.pairs$aa2,
gene.position.cds1$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
selfblast1.dagchainer.input <- cbind(selfblast1.aa1.genepos,
selfblast1.aa2.genepos)
colnames(selfblast1.dagchainer.input) <- c("gene1.chr",
"gene1.seq.id", "gene1.idx1", "gene1.idx2", "gene2.chr",
"gene2.seq.id", "gene2.idx1", "gene2.idx2")
selfblast1.dagchainer.evalue <- selfblast1$crbh1[
match(selfblast1.dagchainer.input$gene1.seq.id,
selfblast1$crbh1$query_id), , drop=FALSE]$evalue
selfblast1.dagchainer.input <- cbind(selfblast1.dagchainer.input,
evalue=selfblast1.dagchainer.evalue)
selfblast1.dagchainer.input$gene1.chr<-paste0("AA1:",
selfblast1.dagchainer.input$gene1.chr)
selfblast1.dagchainer.input$gene2.chr<-paste0("AA1:",
selfblast1.dagchainer.input$gene2.chr)
dagchainer.input <- rbind(dagchainer.input,
selfblast1.dagchainer.input)
}
if(!is.null(selfblast2)){
selfblast2.aa1.genepos <- gene.position.cds2[
match(selfblast2$crbh.pairs$aa1,
gene.position.cds2$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
selfblast2.aa2.genepos <- gene.position.cds2[
match(selfblast2$crbh.pairs$aa2,
gene.position.cds2$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
selfblast2.dagchainer.input <- cbind(selfblast2.aa1.genepos,
selfblast2.aa2.genepos)
colnames(selfblast2.dagchainer.input) <- c("gene1.chr",
"gene1.seq.id", "gene1.idx1", "gene1.idx2", "gene2.chr",
"gene2.seq.id", "gene2.idx1", "gene2.idx2")
selfblast2.dagchainer.evalue <- selfblast2$crbh1[
match(selfblast2.dagchainer.input$gene1.seq.id,
selfblast2$crbh1$query_id), , drop=FALSE]$evalue
selfblast2.dagchainer.input <- cbind(selfblast2.dagchainer.input,
evalue=selfblast2.dagchainer.evalue)
selfblast2.dagchainer.input$gene1.chr<-paste0("AA2:",
selfblast2.dagchainer.input$gene1.chr)
selfblast2.dagchainer.input$gene2.chr<-paste0("AA2:",
selfblast2.dagchainer.input$gene2.chr)
dagchainer.input <- rbind(dagchainer.input,
selfblast2.dagchainer.input)
}
}
tmp <- tempfile()
write.table(dagchainer.input,
sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE, file=tmp)
dagchainercmd <- paste0(dagchainerpath, "run_DAG_chainer.pl")
dagchainerargs <- c(
"-i", tmp,
"-o", sprintf("%0i", gap_open_penalty),
"-e", sprintf("%0i", gap_extension_penalty),
"-g", sprintf("%0i", gap_length),
"-M", sprintf("%0i", max_match_score),
"-D", sprintf("%0i", max_dist_allowed),
"-E", max_evalue,
"-A", sprintf("%0i", min_number_aligned_pairs))
if(selfblast | (!is.null(selfblast1) | !is.null(selfblast2))){
if(ignore_tandem && !only_tandem){
print(paste(dagchainercmd,
paste(dagchainerargs, collapse = " "), "-I", "-s"))
system2(command=dagchainercmd, args=c(dagchainerargs, "-I", "-s"),
stdout=FALSE, stderr=FALSE)
}
if(only_tandem && !ignore_tandem){
print(paste(dagchainercmd,
paste(dagchainerargs, collapse = " "), "-T", "-s"))
system2(command=dagchainercmd, args=c(dagchainerargs, "-T", "-s"),
stdout=FALSE, stderr=FALSE)
}
if(!ignore_tandem && !only_tandem){
print(paste(dagchainercmd,
paste(dagchainerargs, collapse = " "), "-s"))
system2(command=dagchainercmd, args=c(dagchainerargs, "-s"),
stdout=FALSE, stderr=FALSE)
}
} else {
print(paste(dagchainercmd,
paste(dagchainerargs, collapse = " ")))
system2(command=dagchainercmd, args=dagchainerargs,
stdout=FALSE, stderr=FALSE)
}
if(file.info(paste0(tmp, ".aligncoords"))[["size"]]==0){
return(NULL)
}
dagchainer.results <- read.table(paste0(tmp, ".aligncoords"), sep = "\t",
header = FALSE)
dagchainer.groups <- readLines(paste0(tmp, ".aligncoords"))
dagchainer.groups <- dagchainer.groups[grep("num aligned pairs",
dagchainer.groups)]
dagchainer.groups.len <- as.numeric(stringr::str_split_fixed(
stringr::str_split_fixed(dagchainer.groups,
"num aligned pairs: ", 2)[, 2],"\\)", 2)[, 1])
dagchainer.groups.chr1 <- stringr::str_split_fixed(
stringr::str_split_fixed(dagchainer.groups,
"alignment ", 2)[, 2]," ", 2)[, 1]
dagchainer.groups.chr2 <- stringr::str_split_fixed(
stringr::str_split_fixed(dagchainer.groups,
"vs. ", 2)[, 2]," ", 2)[, 1]
dagchainer.groups.idx <- stringr::str_split_fixed(
stringr::str_split_fixed(dagchainer.groups,
"Alignment #", 2)[, 2]," ", 2)[, 1]
dagchainer.groups.idx.reverse <- grep("(reverse)", dagchainer.groups)
dagchainer.groups.id <- paste0(dagchainer.groups.chr1,
":", dagchainer.groups.chr2, ":", dagchainer.groups.idx)
dagchainer.groups.id[dagchainer.groups.idx.reverse] <- paste0(
dagchainer.groups.id[dagchainer.groups.idx.reverse], ".rev")
dagchainer.groups.out <- unlist(apply(cbind(dagchainer.groups.id,
dagchainer.groups.len), 1, function(x) rep(x[1], x[2])))
#if(!selfblast){
# dagchainer.groups.out <- gsub("AA1:", "", dagchainer.groups.out)
# dagchainer.groups.out <- gsub("AA2:", "", dagchainer.groups.out)
#}
if(type=="bp"){
colnames(dagchainer.results) <- c("gene1.chr", "gene1.seq.id",
"gene1.start", "gene1.end", "gene2.chr", "gene2.seq.id",
"gene2.start", "gene2.end", "evalue", "score")
#if(!selfblast){
# dagchainer.results$gene1.chr <- gsub("AA1:", "",
#dagchainer.results$gene1.chr)
# dagchainer.results$gene2.chr <- gsub("AA2:", "",
#dagchainer.results$gene2.chr)
#}
#add gene1.mid and gene2.mid for plotting
dagchainer.results <- dagchainer.results %>%
dplyr::mutate(gene1.mid=gene1.start+((gene1.end - gene1.start)/2),
gene2.mid=gene2.start+((gene2.end - gene2.start)/2)) %>%
dplyr::select(gene1.chr, gene1.seq.id, gene1.start, gene1.end,
gene1.mid, gene2.chr, gene2.seq.id, gene2.start, gene2.end,
gene2.mid, evalue, score)
gene1.idx <- rep(NA, length(dagchainer.results$gene1.chr))
gene2.idx <- rep(NA, length(dagchainer.results$gene2.chr))
#process AA1
gene1.chr.AA1.pos <- which(substr(
dagchainer.results$gene1.chr, 1, 3)=="AA1")
gene2.chr.AA1.pos <- which(substr(
dagchainer.results$gene2.chr, 1, 3)=="AA1")
if(length(gene1.chr.AA1.pos)>0){
gene1.idx[gene1.chr.AA1.pos] <- gene.position.cds1$gene.idx[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
}
if(length(gene2.chr.AA1.pos)>0){
gene2.idx[gene2.chr.AA1.pos] <- gene.position.cds1$gene.idx[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
}
#process AA2
gene1.chr.AA2.pos <- which(substr(
dagchainer.results$gene1.chr, 1, 3)=="AA2")
gene2.chr.AA2.pos <- which(substr(
dagchainer.results$gene2.chr, 1, 3)=="AA2")
if(length(gene1.chr.AA2.pos)>0){
gene1.idx[gene1.chr.AA2.pos] <- gene.position.cds2$gene.idx[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
}
if(length(gene2.chr.AA2.pos)>0){
gene2.idx[gene2.chr.AA2.pos] <- gene.position.cds2$gene.idx[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
}
dagchainer.results <- dagchainer.results %>%
dplyr::mutate(gene1.idx = gene1.idx, gene2.idx = gene2.idx) %>%
dplyr::select(gene1.chr, gene1.seq.id, gene1.start, gene1.end,
gene1.mid, gene1.idx, gene2.chr, gene2.seq.id, gene2.start,
gene2.end, gene2.mid, gene2.idx, evalue, score)
}
if(type=="idx"){
colnames(dagchainer.results) <- c("gene1.chr", "gene1.seq.id",
"gene1.idx1", "gene1.idx2", "gene2.chr", "gene2.seq.id",
"gene2.idx1", "gene2.idx2", "evalue", "score")
#if(!selfblast){
# dagchainer.results$gene1.chr <- gsub("AA1:", "",
#dagchainer.results$gene1.chr)
# dagchainer.results$gene2.chr <- gsub("AA2:", "",
#dagchainer.results$gene2.chr)
#}
#add gene1.mid and gene2.mid for plotting
dagchainer.results <- dagchainer.results %>%
dplyr::mutate(gene1.idx = gene1.idx1, gene2.idx = gene2.idx1) %>%
dplyr::select(gene1.chr, gene1.seq.id, gene1.idx1, gene1.idx2,
gene1.idx, gene2.chr, gene2.seq.id, gene2.idx1, gene2.idx2,
gene2.idx, evalue, score)
gene1.start <- rep(NA, length(dagchainer.results$gene1.chr))
gene2.start <- rep(NA, length(dagchainer.results$gene2.chr))
gene1.end <- rep(NA, length(dagchainer.results$gene1.chr))
gene2.end <- rep(NA, length(dagchainer.results$gene2.chr))
gene1.mid <- rep(NA, length(dagchainer.results$gene1.chr))
gene2.mid <- rep(NA, length(dagchainer.results$gene2.chr))
#process AA1
gene1.chr.AA1.pos <- which(substr(
dagchainer.results$gene1.chr, 1, 3)=="AA1")
gene2.chr.AA1.pos <- which(substr(
dagchainer.results$gene2.chr, 1, 3)=="AA1")
if(length(gene1.chr.AA1.pos)>0){
gene1.start[gene1.chr.AA1.pos] <- gene.position.cds1$gene.start[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
gene1.end[gene1.chr.AA1.pos] <- gene.position.cds1$gene.end[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
gene1.mid[gene1.chr.AA1.pos] <- gene.position.cds1$gene.mid[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
}
if(length(gene2.chr.AA1.pos)>0){
gene2.start[gene2.chr.AA1.pos] <- gene.position.cds1$gene.start[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
gene2.end[gene2.chr.AA1.pos] <- gene.position.cds1$gene.end[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
gene2.mid[gene2.chr.AA1.pos] <- gene.position.cds1$gene.mid[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
}
#process AA2
gene1.chr.AA2.pos <- which(substr(
dagchainer.results$gene1.chr, 1, 3)=="AA2")
gene2.chr.AA2.pos <- which(substr(
dagchainer.results$gene2.chr, 1, 3)=="AA2")
if(length(gene1.chr.AA2.pos)>0){
gene1.start[gene1.chr.AA2.pos] <- gene.position.cds2$gene.start[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
gene1.end[gene1.chr.AA2.pos] <- gene.position.cds2$gene.end[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
gene1.mid[gene1.chr.AA2.pos] <- gene.position.cds2$gene.mid[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
}
if(length(gene2.chr.AA2.pos)>0){
gene2.start[gene2.chr.AA2.pos] <- gene.position.cds2$gene.start[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
gene2.end[gene2.chr.AA2.pos] <- gene.position.cds2$gene.end[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
gene2.mid[gene2.chr.AA2.pos] <- gene.position.cds2$gene.mid[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
}
dagchainer.results <- dagchainer.results %>%
dplyr::mutate(gene1.start=gene1.start,
gene2.start=gene2.start,
gene1.end=gene1.end,
gene2.end=gene2.end,
gene1.mid=gene1.mid,
gene2.mid=gene2.mid) %>%
dplyr::select(gene1.chr, gene1.seq.id, gene1.start, gene1.end,
gene1.mid, gene1.idx, gene2.chr, gene2.seq.id, gene2.start,
gene2.end, gene2.mid, gene2.idx, evalue, score)
}
#add dagchainer group
dagchainer.results <- dagchainer.results %>%
dplyr::mutate(dagchainer_group=dagchainer.groups.out)
attr(dagchainer.results, "CRBHits.class") <- "dagchainer"
attr(dagchainer.results, "selfblast") <- selfblast
if(!is.null(selfblast1) | !is.null(selfblast2)){
attr(dagchainer.results, "selfblast") <- TRUE
}
if(plotDotPlot){
print(plot_dagchainer(dagchainer.results,
DotPlotTitle=DotPlotTitle,
colorBy=colorBy,
kaks=kaks,
ka.max=ka.max,
ks.max=ks.max,
ka.min=ka.min,
ks.min=ks.min,
select.chr=select.chr))
}
return(dagchainer.results)
}
kullrich/CRBHits documentation built on March 29, 2024, 11:34 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions rbh2dagchainer
Documented in rbh2dagchainer
#' @title rbh2dagchainer
#' @name rbh2dagchainer
#' @description This function runs DAGchainer
#' (http://dagchainer.sourceforge.net/) given CRBHit pairs and gene positions
#' for both cds1 and cds2. The default options are set to not compare gene
#' positions in base pairs but instead using gene order (gene.idx).
#' @param rbhpairs (conditional-)reciprocal best hit (CRBHit) pair result
#' (see \code{\link[CRBHits]{cds2rbh}}) [mandatory]
#' @param selfblast1 (conditional-)reciprocal best hit (CRBHit) pair selfblast
#' result for cds1 sequences (see \code{\link[CRBHits]{cds2rbh}}) [optional]
#' @param selfblast2 (conditional-)reciprocal best hit (CRBHit) pair selfblast
#' result for cds2 sequences (see \code{\link[CRBHits]{cds2rbh}}) [optional]
#' @param gene.position.cds1 specify gene position for cds1 sequences
#' (see \code{\link[CRBHits]{cds2genepos}}) [default: NULL]
#' @param gene.position.cds2 specify gene position for cds2 sequences
#' (see \code{\link[CRBHits]{cds2genepos}}) [default: NULL]
#' @param dagchainerpath specify the PATH to the DAGchainer binaries
#' [default: /extdata/dagchainer/]
#' @param gap_open_penalty gap open penalty [default: 0]
#' @param gap_extension_penalty gap extension penalty [default: -3]
#' @param gap_length length of a gap (avgerage distance expected between two
#' syntenic genes); if type is set to "idx" use 1 [default: 10000]
#' @param max_match_score Maximum match score [default: 50]
#' @param max_dist_allowed maximum distance allowed between two matches;
#' if type is set to "idx" use 20 [default: 200000]
#' @param max_evalue Maximum E-value [default: 1e-3]
#' @param ignore_tandem ignore tandem duplicates [default = TRUE]
#' @param only_tandem only tandem alignments [default = FALSE]
#' @param min_number_aligned_pairs Minimum number of Aligned Pairs [default: 5]
#' @param type specify if gene order index "idx" or gene base pair position
#' "bp" should be extracted and used with DAGchainer [default: bp]
#' @param plotDotPlot specify if dotplot should be plotted [default: FALSE]
#' @param DotPlotTitle specify DotPlot title [default: 'DAGchainer results']
#' @param colorBy specify if dagchainer groups should be colored by "Ka", "Ks",
#' "Ka/Ks" or "none" [default: none]
#' @param kaks specify Ka/Ks input obtained via `rbh2kaks()` [default: NULL]
#' @param ka.max specify max Ka to be filtered [default: 5]
#' @param ks.max specify max Ks to be filtered [default: 5]
#' @param ka.min specify min Ka to be filtered [default: 0]
#' @param ks.min specify min Ks to be filtered [default: 0]
#' @param select.chr filter results for chromosome names [default: NULL]
#' @return \code{DAGchanier} results\cr
#' 1: $gene1.chr\cr
#' 2: $gene1.seq.id\cr
#' 3: $gene1.start\cr
#' 4: $gene1.end\cr
#' 5: $gene1.mid\cr
#' 6: $gene1.idx\cr
#' 7: $gene2.chr\cr
#' 8: $gene2.seq.id\cr
#' 9: $gene2.start\cr
#' 10: $gene2.end\cr
#' 11: $gene2.mid\cr
#' 12: $gene2.idx\cr
#' 13: $evalue\cr
#' 14: $score\cr
#' @importFrom tidyr %>%
#' @importFrom dplyr bind_cols select group_by group_map group_keys mutate
#' @importFrom stringr word
#' @importFrom ggplot2 ggplot geom_point geom_abline facet_wrap
#' @importFrom utils write.table
#' @seealso \code{\link[CRBHits]{plot_dagchainer}},
#' \code{\link[CRBHits]{cds2genepos}},
#' \code{\link[CRBHits]{tandemdups}},
#' \code{\link[CRBHits]{rbh2kaks}}
#' @references Haas BJ et al. (2004) DAGchainer: a tool for mining segmental
#' genome duplications and synteny. \emph{Bioinformatics.}
#' \bold{20(18)}, 3643-3646.
#' @examples
#' ## compile dagchainer
#' CRBHits::make_dagchainer()
#' ## load example sequence data
#' data("ath", package="CRBHits")
#' ## get selfhits CRBHit pairs
#' ath_selfhits_crbh <- cds2rbh(
#' cds1=ath,
#' cds2=ath,
#' plotCurve=TRUE)
#' ## get gene position
#' ath.genepos <- cds2genepos(
#' cds=ath,
#' source="ENSEMBL")
#' ## get DAGchainer results
#' ath_selfblast_crbh.dagchainer <- rbh2dagchainer(
#' rbhpairs=ath_selfhits_crbh,
#' gene.position.cds1=ath.genepos,
#' gene.position.cds2=ath.genepos)
#' head(ath_selfblast_crbh.dagchainer)
#' ## plot dagchainer
#' plot_dagchainer(
#' dag=ath_selfblast_crbh.dagchainer)
#' @export rbh2dagchainer
#' @author Kristian K Ullrich
rbh2dagchainer <- function(rbhpairs,
selfblast1=NULL,
selfblast2=NULL,
gene.position.cds1=NULL,
gene.position.cds2=NULL,
dagchainerpath=paste0(find.package("CRBHits"),
"/extdata/dagchainer/"),
gap_open_penalty=0,
gap_extension_penalty=-3,
gap_length=10000,
max_match_score=50,
max_dist_allowed=200000,
max_evalue=1e-3,
ignore_tandem=TRUE,
only_tandem=FALSE,
min_number_aligned_pairs=5,
type="bp",
plotDotPlot=FALSE,
DotPlotTitle="DAGchainer results",
colorBy="none",
kaks=NULL,
ka.max=5,
ks.max=5,
ka.min=0,
ks.min=0,
select.chr=NULL
){
gene.seq.id <- NULL
gene1.seq.id <- NULL
gene2.seq.id <- NULL
gene.chr <- NULL
gene1.chr <- NULL
gene2.chr <- NULL
gene.start <- NULL
gene.end <- NULL
gene.idx <- NULL
gene1.idx1 <- NULL
gene1.idx2 <- NULL
gene2.idx1 <- NULL
gene2.idx2 <- NULL
evalue <- NULL
score <- NULL
if(ignore_tandem == TRUE & only_tandem == TRUE){
stop("both options set to TRUE can not go together. Set one of them to
FALSE")
}
if(attributes(rbhpairs)$CRBHits.class != "crbh"){
stop("Please obtain rbhpairs via the cds2rbh or the cdsfile2rbh
function")
}
if(is.null(gene.position.cds1) | is.null(gene.position.cds2)){
stop("Please provide gene position information. Can be obtained via the
cds2genepos() function")
}
if(!is.null(gene.position.cds1)){
if(attributes(gene.position.cds1)$CRBHits.class != "genepos"){
stop("Please obtain gene position via the cds2genepos() function or
add a 'genepos' class attribute")
}
}
if(!is.null(gene.position.cds2)){
if(attributes(gene.position.cds2)$CRBHits.class != "genepos"){
stop("Please obtain gene position via the cds2genepos() function or
add a 'genepos' class attribute")
}
}
if(!dir.exists(dagchainerpath)){
stop("Error: DAGchainer PATH does not exist. Please specify correct
PATH and/or look into package installation prerequisites. Try to
use make_dagchainer() function.")
}
if(!file.exists(paste0(dagchainerpath, "dagchainer"))){
stop("Error: dagchainer binary does not exist. Please specify correct
PATH and/or look into package installation prerequisites. Try to
use make_dagchainer() function.")
}
if(!file.exists(paste0(dagchainerpath, "run_DAG_chainer.pl"))){
stop("Error: run_DAG_chainer.pl does not exist. Please specify correct
PATH and/or look into package installation prerequisites. Try to use
make_dagchainer() function.")
}
selfblast <- attributes(rbhpairs)$selfblast
genepos.colnames <- c("gene.seq.id", "gene.chr", "gene.start", "gene.end",
"gene.mid", "gene.strand", "gene.idx")
if(plotDotPlot){
if(colorBy == "Ka" | colorBy == "Ks" | colorBy == "Ka/Ks"){
if(is.null(kaks)){
stop("Please provide Ka/Ks input as obtained via rbh2kaks()")
}
if(!is.null(kaks)){
if(attributes(kaks)$CRBHits.class != "kaks"){
stop("Please obtain Ka/Ks input via the rbh2kaks() function
or add a 'kaks' class attribute")
}
}
}
}
if(type=="bp"){
aa1.genepos <- gene.position.cds1[match(rbhpairs$crbh.pairs$aa1,
gene.position.cds1$gene.seq.id), , drop =FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
aa2.genepos <- gene.position.cds2[match(rbhpairs$crbh.pairs$aa2,
gene.position.cds2$gene.seq.id), , drop =FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
dagchainer.input <- cbind(aa1.genepos, aa2.genepos)
colnames(dagchainer.input) <- c("gene1.chr", "gene1.seq.id",
"gene1.start", "gene1.end", "gene2.chr", "gene2.seq.id",
"gene2.start", "gene2.end")
dagchainer.evalue <- rbhpairs$crbh1[match(dagchainer.input$gene1.seq.id,
rbhpairs$crbh1$query_id), , drop=FALSE]$evalue
dagchainer.input <- cbind(dagchainer.input, evalue=dagchainer.evalue)
if(selfblast){
dagchainer.input$gene1.chr<-paste0("AA1:",
dagchainer.input$gene1.chr)
dagchainer.input$gene2.chr<-paste0("AA1:",
dagchainer.input$gene2.chr)
} else{
dagchainer.input$gene1.chr<-paste0("AA1:",
dagchainer.input$gene1.chr)
dagchainer.input$gene2.chr<-paste0("AA2:",
dagchainer.input$gene2.chr)
}
if(!is.null(selfblast1)){
selfblast1.aa1.genepos <- gene.position.cds1[
match(selfblast1$crbh.pairs$aa1,
gene.position.cds1$gene.seq.id), , drop =FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
selfblast1.aa2.genepos <- gene.position.cds1[
match(selfblast1$crbh.pairs$aa2,
gene.position.cds1$gene.seq.id), , drop =FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
selfblast1.dagchainer.input <- cbind(selfblast1.aa1.genepos,
selfblast1.aa2.genepos)
colnames(selfblast1.dagchainer.input) <- c("gene1.chr",
"gene1.seq.id", "gene1.start", "gene1.end", "gene2.chr",
"gene2.seq.id", "gene2.start", "gene2.end")
selfblast1.dagchainer.evalue <- selfblast1$crbh1[
match(selfblast1.dagchainer.input$gene1.seq.id,
selfblast1$crbh1$query_id), , drop=FALSE]$evalue
selfblast1.dagchainer.input <- cbind(selfblast1.dagchainer.input,
evalue=selfblast1.dagchainer.evalue)
selfblast1.dagchainer.input$gene1.chr<-paste0("AA1:",
selfblast1.dagchainer.input$gene1.chr)
selfblast1.dagchainer.input$gene2.chr<-paste0("AA1:",
selfblast1.dagchainer.input$gene2.chr)
dagchainer.input <- rbind(dagchainer.input,
selfblast1.dagchainer.input)
}
if(!is.null(selfblast2)){
selfblast2.aa1.genepos <- gene.position.cds2[
match(selfblast2$crbh.pairs$aa1,
gene.position.cds2$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
selfblast2.aa2.genepos <- gene.position.cds2[
match(selfblast2$crbh.pairs$aa2,
gene.position.cds2$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.start, gene.end)
selfblast2.dagchainer.input <- cbind(selfblast2.aa1.genepos,
selfblast2.aa2.genepos)
colnames(selfblast2.dagchainer.input) <- c("gene1.chr",
"gene1.seq.id", "gene1.start", "gene1.end", "gene2.chr",
"gene2.seq.id", "gene2.start", "gene2.end")
selfblast2.dagchainer.evalue <- selfblast2$crbh1[
match(selfblast2.dagchainer.input$gene1.seq.id,
selfblast2$crbh1$query_id), , drop=FALSE]$evalue
selfblast2.dagchainer.input <- cbind(selfblast2.dagchainer.input,
evalue=selfblast2.dagchainer.evalue)
selfblast2.dagchainer.input$gene1.chr<-paste0("AA2:",
selfblast2.dagchainer.input$gene1.chr)
selfblast2.dagchainer.input$gene2.chr<-paste0("AA2:",
selfblast2.dagchainer.input$gene2.chr)
dagchainer.input <- rbind(dagchainer.input,
selfblast2.dagchainer.input)
}
}
if(type=="idx"){
aa1.genepos <- gene.position.cds1[match(rbhpairs$crbh.pairs$aa1,
gene.position.cds1$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
aa2.genepos <- gene.position.cds2[match(rbhpairs$crbh.pairs$aa2,
gene.position.cds2$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
dagchainer.input <- cbind(aa1.genepos, aa2.genepos)
colnames(dagchainer.input) <- c("gene1.chr", "gene1.seq.id",
"gene1.idx1", "gene1.idx2", "gene2.chr", "gene2.seq.id",
"gene2.idx1", "gene2.idx2")
dagchainer.evalue <- rbhpairs$crbh1[match(dagchainer.input$gene1.seq.id,
rbhpairs$crbh1$query_id), , drop=FALSE]$evalue
dagchainer.input <- cbind(dagchainer.input, evalue=dagchainer.evalue)
if(selfblast){
dagchainer.input$gene1.chr<-paste0("AA1:",
dagchainer.input$gene1.chr)
dagchainer.input$gene2.chr<-paste0("AA1:",
dagchainer.input$gene2.chr)
} else{
dagchainer.input$gene1.chr<-paste0("AA1:",
dagchainer.input$gene1.chr)
dagchainer.input$gene2.chr<-paste0("AA2:",
dagchainer.input$gene2.chr)
}
if(!is.null(selfblast1)){
selfblast1.aa1.genepos <- gene.position.cds1[
match(selfblast1$crbh.pairs$aa1,
gene.position.cds1$gene.seq.id), , drop =FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
selfblast1.aa2.genepos <- gene.position.cds1[
match(selfblast1$crbh.pairs$aa2,
gene.position.cds1$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
selfblast1.dagchainer.input <- cbind(selfblast1.aa1.genepos,
selfblast1.aa2.genepos)
colnames(selfblast1.dagchainer.input) <- c("gene1.chr",
"gene1.seq.id", "gene1.idx1", "gene1.idx2", "gene2.chr",
"gene2.seq.id", "gene2.idx1", "gene2.idx2")
selfblast1.dagchainer.evalue <- selfblast1$crbh1[
match(selfblast1.dagchainer.input$gene1.seq.id,
selfblast1$crbh1$query_id), , drop=FALSE]$evalue
selfblast1.dagchainer.input <- cbind(selfblast1.dagchainer.input,
evalue=selfblast1.dagchainer.evalue)
selfblast1.dagchainer.input$gene1.chr<-paste0("AA1:",
selfblast1.dagchainer.input$gene1.chr)
selfblast1.dagchainer.input$gene2.chr<-paste0("AA1:",
selfblast1.dagchainer.input$gene2.chr)
dagchainer.input <- rbind(dagchainer.input,
selfblast1.dagchainer.input)
}
if(!is.null(selfblast2)){
selfblast2.aa1.genepos <- gene.position.cds2[
match(selfblast2$crbh.pairs$aa1,
gene.position.cds2$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
selfblast2.aa2.genepos <- gene.position.cds2[
match(selfblast2$crbh.pairs$aa2,
gene.position.cds2$gene.seq.id), , drop=FALSE] %>%
dplyr::select(gene.chr, gene.seq.id, gene.idx1=gene.idx,
gene.idx2=gene.idx)
selfblast2.dagchainer.input <- cbind(selfblast2.aa1.genepos,
selfblast2.aa2.genepos)
colnames(selfblast2.dagchainer.input) <- c("gene1.chr",
"gene1.seq.id", "gene1.idx1", "gene1.idx2", "gene2.chr",
"gene2.seq.id", "gene2.idx1", "gene2.idx2")
selfblast2.dagchainer.evalue <- selfblast2$crbh1[
match(selfblast2.dagchainer.input$gene1.seq.id,
selfblast2$crbh1$query_id), , drop=FALSE]$evalue
selfblast2.dagchainer.input <- cbind(selfblast2.dagchainer.input,
evalue=selfblast2.dagchainer.evalue)
selfblast2.dagchainer.input$gene1.chr<-paste0("AA2:",
selfblast2.dagchainer.input$gene1.chr)
selfblast2.dagchainer.input$gene2.chr<-paste0("AA2:",
selfblast2.dagchainer.input$gene2.chr)
dagchainer.input <- rbind(dagchainer.input,
selfblast2.dagchainer.input)
}
}
tmp <- tempfile()
write.table(dagchainer.input,
sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE, file=tmp)
dagchainercmd <- paste0(dagchainerpath, "run_DAG_chainer.pl")
dagchainerargs <- c(
"-i", tmp,
"-o", sprintf("%0i", gap_open_penalty),
"-e", sprintf("%0i", gap_extension_penalty),
"-g", sprintf("%0i", gap_length),
"-M", sprintf("%0i", max_match_score),
"-D", sprintf("%0i", max_dist_allowed),
"-E", max_evalue,
"-A", sprintf("%0i", min_number_aligned_pairs))
if(selfblast | (!is.null(selfblast1) | !is.null(selfblast2))){
if(ignore_tandem && !only_tandem){
print(paste(dagchainercmd,
paste(dagchainerargs, collapse = " "), "-I", "-s"))
system2(command=dagchainercmd, args=c(dagchainerargs, "-I", "-s"),
stdout=FALSE, stderr=FALSE)
}
if(only_tandem && !ignore_tandem){
print(paste(dagchainercmd,
paste(dagchainerargs, collapse = " "), "-T", "-s"))
system2(command=dagchainercmd, args=c(dagchainerargs, "-T", "-s"),
stdout=FALSE, stderr=FALSE)
}
if(!ignore_tandem && !only_tandem){
print(paste(dagchainercmd,
paste(dagchainerargs, collapse = " "), "-s"))
system2(command=dagchainercmd, args=c(dagchainerargs, "-s"),
stdout=FALSE, stderr=FALSE)
}
} else {
print(paste(dagchainercmd,
paste(dagchainerargs, collapse = " ")))
system2(command=dagchainercmd, args=dagchainerargs,
stdout=FALSE, stderr=FALSE)
}
if(file.info(paste0(tmp, ".aligncoords"))[["size"]]==0){
return(NULL)
}
dagchainer.results <- read.table(paste0(tmp, ".aligncoords"), sep = "\t",
header = FALSE)
dagchainer.groups <- readLines(paste0(tmp, ".aligncoords"))
dagchainer.groups <- dagchainer.groups[grep("num aligned pairs",
dagchainer.groups)]
dagchainer.groups.len <- as.numeric(stringr::str_split_fixed(
stringr::str_split_fixed(dagchainer.groups,
"num aligned pairs: ", 2)[, 2],"\\)", 2)[, 1])
dagchainer.groups.chr1 <- stringr::str_split_fixed(
stringr::str_split_fixed(dagchainer.groups,
"alignment ", 2)[, 2]," ", 2)[, 1]
dagchainer.groups.chr2 <- stringr::str_split_fixed(
stringr::str_split_fixed(dagchainer.groups,
"vs. ", 2)[, 2]," ", 2)[, 1]
dagchainer.groups.idx <- stringr::str_split_fixed(
stringr::str_split_fixed(dagchainer.groups,
"Alignment #", 2)[, 2]," ", 2)[, 1]
dagchainer.groups.idx.reverse <- grep("(reverse)", dagchainer.groups)
dagchainer.groups.id <- paste0(dagchainer.groups.chr1,
":", dagchainer.groups.chr2, ":", dagchainer.groups.idx)
dagchainer.groups.id[dagchainer.groups.idx.reverse] <- paste0(
dagchainer.groups.id[dagchainer.groups.idx.reverse], ".rev")
dagchainer.groups.out <- unlist(apply(cbind(dagchainer.groups.id,
dagchainer.groups.len), 1, function(x) rep(x[1], x[2])))
#if(!selfblast){
# dagchainer.groups.out <- gsub("AA1:", "", dagchainer.groups.out)
# dagchainer.groups.out <- gsub("AA2:", "", dagchainer.groups.out)
#}
if(type=="bp"){
colnames(dagchainer.results) <- c("gene1.chr", "gene1.seq.id",
"gene1.start", "gene1.end", "gene2.chr", "gene2.seq.id",
"gene2.start", "gene2.end", "evalue", "score")
#if(!selfblast){
# dagchainer.results$gene1.chr <- gsub("AA1:", "",
#dagchainer.results$gene1.chr)
# dagchainer.results$gene2.chr <- gsub("AA2:", "",
#dagchainer.results$gene2.chr)
#}
#add gene1.mid and gene2.mid for plotting
dagchainer.results <- dagchainer.results %>%
dplyr::mutate(gene1.mid=gene1.start+((gene1.end - gene1.start)/2),
gene2.mid=gene2.start+((gene2.end - gene2.start)/2)) %>%
dplyr::select(gene1.chr, gene1.seq.id, gene1.start, gene1.end,
gene1.mid, gene2.chr, gene2.seq.id, gene2.start, gene2.end,
gene2.mid, evalue, score)
gene1.idx <- rep(NA, length(dagchainer.results$gene1.chr))
gene2.idx <- rep(NA, length(dagchainer.results$gene2.chr))
#process AA1
gene1.chr.AA1.pos <- which(substr(
dagchainer.results$gene1.chr, 1, 3)=="AA1")
gene2.chr.AA1.pos <- which(substr(
dagchainer.results$gene2.chr, 1, 3)=="AA1")
if(length(gene1.chr.AA1.pos)>0){
gene1.idx[gene1.chr.AA1.pos] <- gene.position.cds1$gene.idx[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
}
if(length(gene2.chr.AA1.pos)>0){
gene2.idx[gene2.chr.AA1.pos] <- gene.position.cds1$gene.idx[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
}
#process AA2
gene1.chr.AA2.pos <- which(substr(
dagchainer.results$gene1.chr, 1, 3)=="AA2")
gene2.chr.AA2.pos <- which(substr(
dagchainer.results$gene2.chr, 1, 3)=="AA2")
if(length(gene1.chr.AA2.pos)>0){
gene1.idx[gene1.chr.AA2.pos] <- gene.position.cds2$gene.idx[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
}
if(length(gene2.chr.AA2.pos)>0){
gene2.idx[gene2.chr.AA2.pos] <- gene.position.cds2$gene.idx[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
}
dagchainer.results <- dagchainer.results %>%
dplyr::mutate(gene1.idx = gene1.idx, gene2.idx = gene2.idx) %>%
dplyr::select(gene1.chr, gene1.seq.id, gene1.start, gene1.end,
gene1.mid, gene1.idx, gene2.chr, gene2.seq.id, gene2.start,
gene2.end, gene2.mid, gene2.idx, evalue, score)
}
if(type=="idx"){
colnames(dagchainer.results) <- c("gene1.chr", "gene1.seq.id",
"gene1.idx1", "gene1.idx2", "gene2.chr", "gene2.seq.id",
"gene2.idx1", "gene2.idx2", "evalue", "score")
#if(!selfblast){
# dagchainer.results$gene1.chr <- gsub("AA1:", "",
#dagchainer.results$gene1.chr)
# dagchainer.results$gene2.chr <- gsub("AA2:", "",
#dagchainer.results$gene2.chr)
#}
#add gene1.mid and gene2.mid for plotting
dagchainer.results <- dagchainer.results %>%
dplyr::mutate(gene1.idx = gene1.idx1, gene2.idx = gene2.idx1) %>%
dplyr::select(gene1.chr, gene1.seq.id, gene1.idx1, gene1.idx2,
gene1.idx, gene2.chr, gene2.seq.id, gene2.idx1, gene2.idx2,
gene2.idx, evalue, score)
gene1.start <- rep(NA, length(dagchainer.results$gene1.chr))
gene2.start <- rep(NA, length(dagchainer.results$gene2.chr))
gene1.end <- rep(NA, length(dagchainer.results$gene1.chr))
gene2.end <- rep(NA, length(dagchainer.results$gene2.chr))
gene1.mid <- rep(NA, length(dagchainer.results$gene1.chr))
gene2.mid <- rep(NA, length(dagchainer.results$gene2.chr))
#process AA1
gene1.chr.AA1.pos <- which(substr(
dagchainer.results$gene1.chr, 1, 3)=="AA1")
gene2.chr.AA1.pos <- which(substr(
dagchainer.results$gene2.chr, 1, 3)=="AA1")
if(length(gene1.chr.AA1.pos)>0){
gene1.start[gene1.chr.AA1.pos] <- gene.position.cds1$gene.start[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
gene1.end[gene1.chr.AA1.pos] <- gene.position.cds1$gene.end[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
gene1.mid[gene1.chr.AA1.pos] <- gene.position.cds1$gene.mid[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
}
if(length(gene2.chr.AA1.pos)>0){
gene2.start[gene2.chr.AA1.pos] <- gene.position.cds1$gene.start[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
gene2.end[gene2.chr.AA1.pos] <- gene.position.cds1$gene.end[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
gene2.mid[gene2.chr.AA1.pos] <- gene.position.cds1$gene.mid[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA1.pos],
gene.position.cds1$gene.seq.id)]
}
#process AA2
gene1.chr.AA2.pos <- which(substr(
dagchainer.results$gene1.chr, 1, 3)=="AA2")
gene2.chr.AA2.pos <- which(substr(
dagchainer.results$gene2.chr, 1, 3)=="AA2")
if(length(gene1.chr.AA2.pos)>0){
gene1.start[gene1.chr.AA2.pos] <- gene.position.cds2$gene.start[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
gene1.end[gene1.chr.AA2.pos] <- gene.position.cds2$gene.end[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
gene1.mid[gene1.chr.AA2.pos] <- gene.position.cds2$gene.mid[
match(dagchainer.results$gene1.seq.id[gene1.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
}
if(length(gene2.chr.AA2.pos)>0){
gene2.start[gene2.chr.AA2.pos] <- gene.position.cds2$gene.start[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
gene2.end[gene2.chr.AA2.pos] <- gene.position.cds2$gene.end[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
gene2.mid[gene2.chr.AA2.pos] <- gene.position.cds2$gene.mid[
match(dagchainer.results$gene2.seq.id[gene2.chr.AA2.pos],
gene.position.cds2$gene.seq.id)]
}
dagchainer.results <- dagchainer.results %>%
dplyr::mutate(gene1.start=gene1.start,
gene2.start=gene2.start,
gene1.end=gene1.end,
gene2.end=gene2.end,
gene1.mid=gene1.mid,
gene2.mid=gene2.mid) %>%
dplyr::select(gene1.chr, gene1.seq.id, gene1.start, gene1.end,
gene1.mid, gene1.idx, gene2.chr, gene2.seq.id, gene2.start,
gene2.end, gene2.mid, gene2.idx, evalue, score)
}
#add dagchainer group
dagchainer.results <- dagchainer.results %>%
dplyr::mutate(dagchainer_group=dagchainer.groups.out)
attr(dagchainer.results, "CRBHits.class") <- "dagchainer"
attr(dagchainer.results, "selfblast") <- selfblast
if(!is.null(selfblast1) | !is.null(selfblast2)){
attr(dagchainer.results, "selfblast") <- TRUE
}
if(plotDotPlot){
print(plot_dagchainer(dagchainer.results,
DotPlotTitle=DotPlotTitle,
colorBy=colorBy,
kaks=kaks,
ka.max=ka.max,
ks.max=ks.max,
ka.min=ka.min,
ks.min=ks.min,
select.chr=select.chr))
}
return(dagchainer.results)
}
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