/usr/lib/R/site-library/rtracklayer/unitTests/test_wig.R is in r-bioc-rtracklayer 1.38.0-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 | test_wig <- function() {
test_path <- system.file("tests", package = "rtracklayer")
test_wig <- file.path(test_path, "step.wig")
createCorrectGR <- function(si) {
score <- c(seq(10, 20, by = 2.5), seq(17.5, 10, by = -2.5),
seq(1000, 100, by = -100))
start <- c(59104701 + cumsum(c(0, 200, 500, 200, 300, 180, 220, 390, 1180)),
59108021 + cumsum(c(0, rep(300, 9))))
width <- c(rep(1, 9), rep(200, 10))
space <- factor(c(rep("chr19", 9), rep("chr18", 10)), seqlevels(si))
correct_gr <- GRanges(space, IRanges(start, width = width), score = score)
if (!any(is.na(genome(si))))
genome(correct_gr) <- unname(genome(si)[1])
seqinfo(correct_gr) <- si
correct_gr
}
createCorrectUCSC <- function(gr) {
track_line <- new("GraphTrackLine", type = "wig", name = "test",
description = "test track", visibility = "full",
autoScale = FALSE, viewLimits = c(0, 1000),
color = c(0L, 200L, 100L),
maxHeightPixels = c(100L, 50L, 20L),
graphType = "points", priority = 30)
new("UCSCData", gr, trackLine = track_line)
}
correct_gr <- createCorrectGR(Seqinfo(c("chr19", "chr18")))
correct_ucsc <- createCorrectUCSC(correct_gr)
## TEST: basic import
test <- import(test_wig)
checkIdentical(correct_ucsc, test)
test <- import.wig(test_wig)
checkIdentical(correct_ucsc, test)
test_wig_file <- WIGFile(test_wig)
checkException(import(test_wig_file, format = "bed"))
test <- import(test_wig_file, format = "wig")
checkIdentical(correct_ucsc, test)
test <- import(test_wig_file)
checkIdentical(correct_ucsc, test)
test_wig_con <- file(test_wig)
test <- import(test_wig_con, format = "wig")
checkIdentical(correct_ucsc, test)
test_wig_con <- file(test_wig)
test <- import(WIGFile(test_wig_con))
checkIdentical(correct_ucsc, test)
## TEST: 'genome'
hg19_seqinfo <- SeqinfoForBSGenome("hg19")
correct_genome <- createCorrectUCSC(createCorrectGR(hg19_seqinfo))
test <- import(test_wig, genome = "hg19")
checkIdentical(correct_genome, test)
## TEST: trackLine = FALSE
test <- import(test_wig, trackLine = FALSE)
checkIdentical(correct_gr, test)
## TEST: which
which <- correct_gr[3:4]
correct_which <- subsetByOverlaps(correct_ucsc, which)
test <- import(test_wig, which = which)
checkIdentical(correct_which, test)
## TEST: basic export
test_wig_out <- file.path(tempdir(), "test.wig")
on.exit(unlink(test_wig_out))
export(correct_ucsc, test_wig_out)
test <- import(test_wig_out)
checkIdentical(correct_ucsc, test)
export.wig(correct_ucsc, test_wig_out)
test <- import(test_wig_out)
checkIdentical(correct_ucsc, test)
test_foo_out <- file.path(tempdir(), "test.foo")
export(correct_ucsc, test_foo_out, format = "wig")
on.exit(unlink(test_foo_out))
test <- import(test_wig_out)
checkIdentical(correct_ucsc, test)
test_wig_out_file <- WIGFile(test_wig_out)
export(correct_ucsc, test_wig_out_file)
test <- import(test_wig_out)
checkIdentical(correct_ucsc, test)
checkException(export(correct_ucsc, test_wig_out_file, format = "gff"))
## TEST: append
correct_ucsc2 <- initialize(correct_ucsc,
trackLine = initialize(correct_ucsc@trackLine,
name = "test2"))
export(correct_ucsc2, test_wig_out_file, append = TRUE)
test <- import(test_wig_out_file)
correct_list <- GenomicRangesList(test = correct_ucsc,
test2 = correct_ucsc2)
checkIdentical(correct_list, test)
## TEST: track line parameters
export(correct_ucsc, test_wig_out, name = "test2")
test <- import(test_wig_out)
checkIdentical(correct_ucsc2, test)
## TEST: export trackLine
export(correct_ucsc, test_wig_out, trackLine = FALSE)
test <- import(test_wig_out)
checkIdentical(test, correct_gr)
## TEST: Plain GRanges / bedGraph
export.ucsc(correct_gr, test_wig_out) # mixture of steps leads to bedGraph
test <- import(test_wig_out)
default_line <- new("GraphTrackLine", name = "R Track", type = "bedGraph")
correct_default <- new("UCSCData", correct_gr, trackLine = default_line)
checkIdentical(test, correct_default)
correct_chr18 <- keepSeqlevels(correct_gr, "chr18", pruning.mode="coarse")
export.ucsc(correct_chr18, test_wig_out)
test <- import(test_wig_out)
default_line <- new("GraphTrackLine", name = "R Track", type = "wig")
correct_default <- new("UCSCData",
keepSeqlevels(correct_gr, "chr18",
pruning.mode="coarse"),
trackLine = default_line)
checkIdentical(test, correct_default)
## TEST: GenomicRangesList
export(correct_list, test_wig_out)
test <- import(test_wig_out)
checkIdentical(correct_list, test)
## TEST: gzip
test_wig_gz <- paste(test_wig_out, ".gz", sep = "")
on.exit(unlink(test_wig_gz))
export(correct_ucsc, test_wig_gz)
test <- import(test_wig_gz)
checkIdentical(correct_ucsc, test)
export(correct_ucsc2, test_wig_gz, append = TRUE)
test <- import(test_wig_gz)
checkIdentical(correct_list, test)
## TEST: Using connection to add comment header
test_wig_con <- file(test_wig_out)
open(test_wig_con, "w")
comment <- "# test comment"
writeLines(comment, test_wig_con)
export(correct_ucsc, test_wig_con)
close(test_wig_con)
checkIdentical(comment, readLines(test_wig_out, n = 1))
test <- import(test_wig_out)
checkIdentical(correct_ucsc, test)
}
|