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test_that("test_searchSeq", {
library(IRanges)
library(Biostrings)
data(MA0003.2)
data(MA0004.1)
pwm1 <- toPWM(MA0003.2)
pwm2 <- toPWM(MA0004.1)
pwmList <- PWMatrixList(pwm1 = pwm1, pwm2 = pwm2)
seq1 <- "GAATTCTCTCTTGTTGTAGCATTGCCTCAGGGCACACGTGCAAAATG"
seq2 <- "GTTTCACCATTGCCTCAGGGCATAAATATATAAAAAAATATAATTTTCATC"
siteset <- searchSeq(pwm1, seq1, seqname = "seq1", strand = "*",
min.score = "80%")
expect_identical(3L, length(siteset))
siteset <- searchSeq(pwm1, seq1, seqname = "seq1", strand = "+",
min.score = "80%")
expect_identical(1L, length(siteset))
siteset <- searchSeq(pwm1, seq1, seqname = "seq1", strand = "-",
min.score = "80%")
expect_identical(2L, length(siteset))
seqs <- DNAStringSet(c(seq1 = seq1, seq2 = seq2))
sitesetList <- searchSeq(pwmList, seqs, min.score = "80%")
expect_identical(IRanges(start = c(20L, 22L, 23L, 8L, 10L,
11L, 35L, 35L), end = c(34L, 36L, 37L, 22L, 24L, 25L,
40L, 40L)), ranges(unname(as(sitesetList, "GRanges"))))
})
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