/usr/lib/R/site-library/ShortRead/unitTests/test_ShortRead.R is in r-bioc-shortread 1.36.0-1.
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 | sp <- SolexaPath(system.file("extdata", package="ShortRead"))
sr <- as(readFastq(sp, "s_1_sequence.txt"), "ShortRead")
.equals <- function(x, y)
{
checkIdentical(as.character(sread(x)), as.character(sread(y)))
checkIdentical(as.character(id(x)), as.character(id(y)))
}
test_ShortRead_construction <- function() {
obj <- ShortRead()
checkTrue(class(obj) == "ShortRead")
checkTrue(validObject(obj))
obj <- ShortRead(sread(sr))
checkTrue(class(obj) == "ShortRead")
checkTrue(validObject(obj))
.equals(new("ShortRead", sread=DNAStringSet(sread(sr)),
id=BStringSet(rep("", length(sr)))), obj)
obj <- ShortRead(sread(sr), id(sr))
checkTrue(class(obj) == "ShortRead")
checkTrue(validObject(obj))
.equals(sr, obj)
}
test_ShortRead_narrow <- function() {
obj <- narrow(sr, start=1, end=10)
checkTrue(class(obj) == "ShortRead")
checkTrue(length(obj) == length(sr))
checkTrue(unique(width(obj)) == 10)
checkIdentical(as.character(sread(obj)),
substr(as.character(sread(sr)), 1, 10))
checkIdentical(narrow(sr, start=start(sread(sr))), sr)
}
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