| ... | ... |
@@ -98,4 +98,25 @@ setMethod("syntenicDotplot", signature=(x="Axt"),
|
| 98 | 98 |
firstChrs=firstChrs, |
| 99 | 99 |
secondChrs=secondChrs, |
| 100 | 100 |
col=col, type=type) |
| 101 |
- }) |
|
| 102 | 101 |
\ No newline at end of file |
| 102 |
+ }) |
|
| 103 |
+ |
|
| 104 |
+### ----------------------------------------------------------------- |
|
| 105 |
+### makeAxtTracks |
|
| 106 |
+### Exported!! |
|
| 107 |
+makeAxtTracks <- function(x){
|
|
| 108 |
+ if(!is(x, "Axt")){
|
|
| 109 |
+ stop(deparse(substitute(x)), " must be a `Axt`` class!") |
|
| 110 |
+ } |
|
| 111 |
+ x <- fixCoordinates(x) |
|
| 112 |
+ |
|
| 113 |
+ targetAxt <- targetRanges(x) |
|
| 114 |
+ queryAxt <- queryRanges(x) |
|
| 115 |
+ |
|
| 116 |
+ targetAxt$name <- as.character(queryAxt) |
|
| 117 |
+ queryAxt$name <- as.character(targetAxt) |
|
| 118 |
+ |
|
| 119 |
+ export.bed(targetAxt, "targetAxt.bed") |
|
| 120 |
+ export.bed(queryAxt, "queryAxt.bed") |
|
| 121 |
+ |
|
| 122 |
+ invisible(list(targetAxt, queryAxt)) |
|
| 123 |
+} |
| ... | ... |
@@ -375,56 +375,3 @@ blatCNE <- function(cne, blatOptions=NULL, cutIdentity=90){
|
| 375 | 375 |
as.integer(CNEqNameIndex) <= cutoffs2] |
| 376 | 376 |
BiocGenerics:::replaceSlots(cne, CNEFinal=cneFinal) |
| 377 | 377 |
} |
| 378 |
- |
|
| 379 |
-# ceScanOneStep <- function(axt1, filter1=NULL, sizes1, assembly1, twoBit1, |
|
| 380 |
-# axt2, filter2=NULL, sizes2, assembly2, twoBit2, |
|
| 381 |
-# thresholds=c("49_50"),
|
|
| 382 |
-# blatBinary="blat", |
|
| 383 |
-# blatCutoff1, blatCutoff2 |
|
| 384 |
-# ){
|
|
| 385 |
-# if(grepl("_", assembly1) || grepl("_", assembly2))
|
|
| 386 |
-# stop("The assembly name must not contain \"_\"")
|
|
| 387 |
-# if(assembly1 < assembly2){
|
|
| 388 |
-# .ceScanSwap(axt1=axt1, filter1=filter1, sizes1=sizes1, assembly1=assembly1, |
|
| 389 |
-# twoBit1=twoBit1, axt2=axt2, filter2=filter2, sizes2=sizes2, |
|
| 390 |
-# assembly2=assembly2, twoBit2=twoBit2, thresholds=thresholds, |
|
| 391 |
-# blatBinary=blatBinary, blatCutoff1=blatCutoff1, |
|
| 392 |
-# blatCutoff2=blatCutoff2) |
|
| 393 |
-# }else{
|
|
| 394 |
-# .ceScanSwap(axt1=axt2, filter1=filter2, sizes1=sizes2, assembly1=assembly2, |
|
| 395 |
-# twoBit1=twoBit2, axt2=axt1, filter2=filter1, |
|
| 396 |
-# sizes2=sizes1, assembly2=assembly1, twoBit2=twoBit1, |
|
| 397 |
-# thresholds=thresholds, blatBinary=blatBinary, |
|
| 398 |
-# blatCutoff1=blatCutoff2, blatCutoff2=blatCutoff1) |
|
| 399 |
-# } |
|
| 400 |
-# } |
|
| 401 |
-# |
|
| 402 |
-# .ceScanSwap <- function(axt1, filter1=NULL, sizes1, assembly1, twoBit1, |
|
| 403 |
-# axt2, filter2=NULL, sizes2, assembly2, twoBit2, |
|
| 404 |
-# thresholds=c("49_50"),
|
|
| 405 |
-# blatBinary="blat", |
|
| 406 |
-# blatCutoff1, blatCutoff2 |
|
| 407 |
-# ){
|
|
| 408 |
-# ## In this function, we make sure "assembly1" is smaller than "assembly2". |
|
| 409 |
-# ## danRer7 is smaller than hg19. |
|
| 410 |
-# ## This is just for easier database storage table name: "danRer7_hg19_49_50" |
|
| 411 |
-# CNE1 <- ceScan(axt1, filter1, filter2, sizes2, thresholds) |
|
| 412 |
-# CNE2 <- ceScan(axt2, filter2, filter1, sizes1, thresholds) |
|
| 413 |
-# CNEMerged <- mapply(cneMerge, CNE1, CNE2, SIMPLIFY=FALSE) |
|
| 414 |
-# names(CNEMerged) = paste(assembly1, assembly2, thresholds, sep="_") |
|
| 415 |
-# CNEBlated <- list() |
|
| 416 |
-# for(i in 1:length(CNEMerged)){
|
|
| 417 |
-# CNEBlated[[names(CNEMerged)[i]]] <- |
|
| 418 |
-# blatCNE(CNEMerged[[i]], as.integer(sub(".+_.+_\\d+_", "",
|
|
| 419 |
-# names(CNEMerged)[i])), |
|
| 420 |
-# cutoffs1=blatCutoff1, cutoffs2=blatCutoff2, |
|
| 421 |
-# assembly1Twobit=twoBit1, assembly2Twobit=twoBit2, |
|
| 422 |
-# blatBinary=blatBinary) |
|
| 423 |
-# } |
|
| 424 |
-# ans <- CNE(assembly1=assembly1, assembly2=assembly2, |
|
| 425 |
-# thresholds=thresholds, |
|
| 426 |
-# CNE1=CNE1, CNE2=CNE2, CNEMerged=CNEMerged, |
|
| 427 |
-# CNERepeatsFiltered=CNEBlated, |
|
| 428 |
-# alignMethod=blatBinary) |
|
| 429 |
-# return(ans) |
|
| 430 |
-# } |
| 100 | 101 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,43 @@ |
| 1 |
+\name{makeAxtTracks}
|
|
| 2 |
+\alias{makeAxtTracks}
|
|
| 3 |
+\title{
|
|
| 4 |
+ makeAxtTracks |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+ Make the bed tracks for the \sQuote{Axt} alignment.
|
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+ makeAxtTracks(x) |
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ \item{x}{
|
|
| 14 |
+ A \code{Axt} object.
|
|
| 15 |
+ } |
|
| 16 |
+} |
|
| 17 |
+\details{
|
|
| 18 |
+ The coordinates of query \sQuote{Axt} alignment are fixed to be relative to
|
|
| 19 |
+ positive strand before output into \sQuote{bed} file.
|
|
| 20 |
+} |
|
| 21 |
+\value{
|
|
| 22 |
+ A list of GRanges for target and query alignments. |
|
| 23 |
+ The two output \sQuote{bed} files are
|
|
| 24 |
+ \dQuote{targetAxt.bed} and \dQuote{queryAxt.bed}.
|
|
| 25 |
+} |
|
| 26 |
+\author{
|
|
| 27 |
+ Ge Tan |
|
| 28 |
+} |
|
| 29 |
+\seealso{
|
|
| 30 |
+ \code{\link{fixCoordinates}}
|
|
| 31 |
+} |
|
| 32 |
+\examples{
|
|
| 33 |
+ tAssemblyFn <- file.path(system.file("extdata",
|
|
| 34 |
+ package="BSgenome.Drerio.UCSC.danRer10"), |
|
| 35 |
+ "single_sequences.2bit") |
|
| 36 |
+ qAssemblyFn <- file.path(system.file("extdata",
|
|
| 37 |
+ package="BSgenome.Hsapiens.UCSC.hg38"), |
|
| 38 |
+ "single_sequences.2bit") |
|
| 39 |
+ axtFn <- file.path(system.file("extdata", package="CNEr"),
|
|
| 40 |
+ "danRer10.hg38.net.axt") |
|
| 41 |
+ axt <- readAxt(axtFn, tAssemblyFn, qAssemblyFn) |
|
| 42 |
+ makeAxtTracks(axt) |
|
| 43 |
+} |
| ... | ... |
@@ -153,4 +153,21 @@ test_that("test_subAxt", {
|
| 153 | 153 |
ans <- psubAxt(axt, targetSearch, querySearch) |
| 154 | 154 |
expect_identical(ans, axt[c(1,3,347:350)]) |
| 155 | 155 |
} |
| 156 |
-) |
|
| 157 | 156 |
\ No newline at end of file |
| 157 |
+) |
|
| 158 |
+ |
|
| 159 |
+test_that("test_makeAxtTracks", {
|
|
| 160 |
+ tAssemblyFn <- file.path(system.file("extdata",
|
|
| 161 |
+ package="BSgenome.Drerio.UCSC.danRer10"), |
|
| 162 |
+ "single_sequences.2bit") |
|
| 163 |
+ qAssemblyFn <- file.path(system.file("extdata",
|
|
| 164 |
+ package="BSgenome.Hsapiens.UCSC.hg38"), |
|
| 165 |
+ "single_sequences.2bit") |
|
| 166 |
+ axtFn <- file.path(system.file("extdata", package="CNEr"),
|
|
| 167 |
+ "danRer10.hg38.net.axt") |
|
| 168 |
+ axt <- readAxt(axtFn, tAssemblyFn, qAssemblyFn) |
|
| 169 |
+ ans <- makeAxtTracks(axt) |
|
| 170 |
+ |
|
| 171 |
+ ## Make sure the coordinates are right. |
|
| 172 |
+ expect_identical(ans[[1]]$name[1:2], c("chr7:12578221-12578959:-",
|
|
| 173 |
+ "chr9:121302901-121303067:-")) |
|
| 174 |
+}) |
