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test_that("test_Axt", {
library(GenomicRanges)
library(Biostrings)
targetRanges <- GRanges(seqnames=c("chr1", "chr1", "chr2", "chr3"),
ranges=IRanges(start=c(1, 20, 2, 3),
end=c(10, 25, 10, 10)),
strand="+")
targetSeqs <- DNAStringSet(c("ATTTTATGTG", "GGGAAG", "GGGCTTTTG",
"TTGTGTAG"))
queryRanges <- GRanges(seqnames=c("chr1", "chr10", "chr10", "chr20"),
ranges=IRanges(start=c(1, 25, 50, 5),
end=c(10, 30, 58, 12)),
strand="+")
querySeqs <- DNAStringSet(c("ATTTAAAGTG", "GGAAAA", "GGGCTCTGG", "TTAAATAA"))
score <- c(246L, 4422L, 5679L, 1743L)
symCount <- c(10L, 6L, 9L, 8L)
axt <- Axt(targetRanges=targetRanges, targetSeqs=targetSeqs,
queryRanges=queryRanges, querySeqs=querySeqs,
score=score, symCount=symCount)
# Test the validity
## test the different lengths
expect_error(Axt(targetRanges=targetRanges, targetSeqs=targetSeqs,
queryRanges=queryRanges, querySeqs=querySeqs,
score=score, symCount=symCount[1:3]))
expect_error(Axt(targetRanges=targetRanges, targetSeqs=targetSeqs,
queryRanges=queryRanges, querySeqs=querySeqs,
score=score[1:3], symCount=symCount))
expect_error(Axt(targetRanges=targetRanges[1:3], targetSeqs=targetSeqs[1:3],
queryRanges=queryRanges, querySeqs=querySeqs,
score=score, symCount=symCount))
expect_error(Axt(targetRanges=targetRanges, targetSeqs=targetSeqs,
queryRanges=queryRanges[1:3], querySeqs=querySeqs[1:3],
score=score, symCount=symCount))
## test the inconsistent widths
expect_error(Axt(targetRanges=targetRanges, targetSeqs=targetSeqs,
queryRanges=queryRanges, querySeqs=querySeqs,
score=score, symCount=c(10L, 6L, 9L, 9L)))
expect_error(Axt(targetRanges=targetRanges,
targetSeqs= DNAStringSet(c("ATTTTATGTG", "GGGAAG",
"GGGCTTTTG","TTGTGTA")),
queryRanges=queryRanges, querySeqs=querySeqs,
score=score, symCount=symCount))
# Test the getters and setters
## test length
expect_identical(length(axt), 4L)
## test targetRanges, targetSeqs
expect_equivalent(targetRanges(axt), targetRanges)
expect_identical(targetSeqs(axt), targetSeqs)
## test queryRanges, querySeqs
expect_equivalent(queryRanges(axt), queryRanges)
expect_identical(querySeqs(axt), querySeqs)
## test score, symCount
expect_identical(score(axt), score)
expect_identical(symCount(axt), symCount)
# TODO: Test matchDistr
## matchDistr
# Test Vector methods
expect_identical(length(axt[1:2]), 2L)
# test combing
expect_identical(length(c(axt, axt)), 8L)
}
)
test_that("test_subAxt", {
library(GenomicRanges)
library(rtracklayer)
skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
tAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit")
qAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
axtFilesHg38DanRer10 <- file.path(system.file("extdata", package="CNEr"),
"hg38.danRer10.net.axt")
axtHg38DanRer10 <- readAxt(axtFilesHg38DanRer10, tAssemblyFn, qAssemblyFn)
## Test selection on target sequence
axt <- subAxt(axtHg38DanRer10, chr="chr1", start=148165963L, end=222131835L,
select="target")
expect_identical(length(axt), 2L)
## Test selection on query sequence
searchGRanges <- GRanges(seqnames="chr6",
ranges=IRanges(start=25825774,
end=26745499),
strand="+")
axt <- subAxt(axtHg38DanRer10, searchGRanges, select="query")
expect_identical(length(axt), 9L)
})
# test_that("test_summaryAxt", {
# axtFilesHg38DanRer10 <- file.path(system.file("extdata", package="CNEr"),
# "hg38.danRer10.net.axt")
# axtHg38DanRer10 <- readAxt(axtFilesHg38DanRer10)
# ans <- summary(axtHg38DanRer10)
# # expect_equal(as.integer(ans),
# # c(907L, 5012L, 1133L, 3274L, 1801L, 1606L, 3078L))
# }
# )
test_that("test_fixCoordinates", {
skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
axtFnDanRer10Hg38 <- file.path(system.file("extdata", package="CNEr"),
"danRer10.hg38.net.axt")
qAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit")
tAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
axtDanRer10Hg38 <- readAxt(axtFnDanRer10Hg38, tAssemblyFn=tAssemblyFn,
qAssemblyFn=qAssemblyFn)
fixedAxt <- fixCoordinates(axtDanRer10Hg38)
# Test the restore
expect_identical(fixCoordinates(fixedAxt), axtDanRer10Hg38)
# Test that targetRanges are intact
expect_identical(targetRanges(fixedAxt), targetRanges(axtDanRer10Hg38))
# Test the fixed queryRanges coordinates.
queryRangesTest <- queryRanges(fixedAxt)[1:3]
expect_identical(ranges(queryRangesTest), IRanges(start=c(12578221, 121302901,
12577855),
end=c(12578959, 121303067,
12578037))
)
}
)
test_that("test_subAxt", {
skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
tAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
qAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit")
axtFn <- file.path(system.file("extdata", package="CNEr"),
"danRer10.hg38.net.axt")
axt <- readAxt(axtFn, tAssemblyFn, qAssemblyFn)
targetSearch <- GRanges(seqnames=c("chr6"),
ranges=IRanges(start=c(24000000, 26900000),
end=c(24060000, 26905000)),
strand="+"
)
querySearch <- GRanges(seqnames=c("chr7", "chr2"),
ranges=IRanges(start=c(12577000, 241262700),
end=c(12579000, 241268600)),
strand="+"
)
ans <- psubAxt(axt, targetSearch, querySearch)
expect_identical(ans, axt[c(1,3,347:350)])
}
)
test_that("test_makeAxtTracks", {
skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
tAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
qAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit")
axtFn <- file.path(system.file("extdata", package="CNEr"),
"danRer10.hg38.net.axt")
axt <- readAxt(axtFn, tAssemblyFn, qAssemblyFn)
ans <- makeAxtTracks(axt)
## Make sure the coordinates are right.
expect_identical(ans[[1]]$name[1:2], c("chr7:12578221-12578959:-",
"chr9:121302901-121303067:-"))
})
|
