/usr/lib/R/site-library/Biostrings/unitTests/test_MultipleAlignment.R is in r-bioc-biostrings 2.42.1-1.
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{
c(string1 = "AAGGTCTCCA-GCCTGCCCTTCAGTGTGGAGGCGCTCATG--TCGGACA",
string2 = "AAGGTCTCCA-GCCTGCCCTTCAGCGTGGAGGCGCTCATG--TCCGACA",
string3 = "CATTTATATATGGTCCCCCTCCCCCCAAGAAACACACATAGTTTTGACA")
}
make_DNAMultipleAlignment <- function()
{
DNAMultipleAlignment(strings_DNAMultipleAlignment())
}
test_DNAMultipleAlignment_empty <- function()
{
malign <- DNAMultipleAlignment()
checkTrue(validObject(malign, test=TRUE, complete=TRUE))
checkIdentical(as.character(unmasked(malign)), as.character(DNAStringSet()))
checkIdentical(rownames(malign), NULL)
checkIdentical(rowmask(malign), new("NormalIRanges"))
checkIdentical(colmask(malign), new("NormalIRanges"))
checkIdentical(as.character(maskMotif(malign, "GC")), character())
checkIdentical(as.character(maskGaps(malign)), character())
checkIdentical(nrow(malign), 0L)
checkIdentical(ncol(malign), 0L)
checkIdentical(dim(malign), c(0L, 0L))
checkIdentical(maskednrow(malign), 0L)
checkIdentical(maskedncol(malign), 0L)
checkIdentical(maskeddim(malign), c(0L, 0L))
checkIdentical(maskedratio(malign), c(0L/0L, 0L/0L))
checkIdentical(nchar(malign), 0L)
checkIdentical(seqtype(malign), "DNA")
checkIdentical(as.character(malign), character(0))
checkIdentical(consensusMatrix(malign),
matrix(integer(), nrow=length(DNA_ALPHABET), ncol=0,
dimnames=list(DNA_ALPHABET, NULL)))
checkIdentical(consensusString(malign), character())
checkIdentical(as.character(consensusViews(malign)), character())
checkIdentical(alphabetFrequency(malign),
matrix(integer(), nrow=0, ncol=length(DNA_ALPHABET),
dimnames=list(NULL, DNA_ALPHABET)))
checkIdentical(alphabetFrequency(malign, collapse=TRUE),
structure(integer(length(DNA_ALPHABET)), names=DNA_ALPHABET))
}
test_DNAMultipleAlignment_unnamed <- function()
{
malign <- make_DNAMultipleAlignment()
rownames(malign) <- NULL
checkTrue(validObject(malign, test=TRUE))
checkIdentical(as.character(unmasked(malign)),
unname(strings_DNAMultipleAlignment()))
checkIdentical(rownames(malign), NULL)
checkIdentical(rowmask(malign), new("NormalIRanges"))
checkIdentical(colmask(malign), new("NormalIRanges"))
checkIdentical(as.character(maskMotif(malign, "GC", fixed=FALSE)),
c("AAGGTCTCCA-TCCTTCAGTGGAGTCATG--TCGGACA",
"AAGGTCTCCA-TCCTTCAGTGGAGTCATG--TCCGACA",
"CATTTATATATCCCTCCCCAAGAAACATAGTTTTGACA"))
checkIdentical(as.character(maskGaps(malign)),
unname(strings_DNAMultipleAlignment()))
checkIdentical(nrow(malign), length(strings_DNAMultipleAlignment()))
checkIdentical(ncol(malign), nchar(strings_DNAMultipleAlignment())[[1]])
checkIdentical(dim(malign),
c(length(strings_DNAMultipleAlignment()),
nchar(strings_DNAMultipleAlignment())[[1]]))
checkIdentical(maskednrow(malign), 0L)
checkIdentical(maskedncol(malign), 0L)
checkIdentical(maskeddim(malign), c(0L, 0L))
checkIdentical(maskedratio(malign), c(0, 0))
checkIdentical(nchar(malign), nchar(strings_DNAMultipleAlignment())[[1]])
checkIdentical(seqtype(malign), "DNA")
checkIdentical(as.character(malign), unname(strings_DNAMultipleAlignment()))
checkIdentical(consensusMatrix(malign)[1:4, 1:4],
rbind(A=c(2L,3L,0L,0L),
C=c(1L,0L,0L,0L),
G=c(0L,0L,2L,2L),
T=c(0L,0L,1L,1L)))
checkIdentical(consensusString(malign),
"MAKKTMTMYA-GSYYSCCCTYCMSYSWRGARRCRCWCATR--TYBGACA")
checkIdentical(as.character(consensusViews(malign)),
"MAKKTMTMYA-GSYYSCCCTYCMSYSWRGARRCRCWCATR--TYBGACA")
checkIdentical(alphabetFrequency(malign)[,1:4],
cbind(A=c(8L,8L,15L),
C=c(14L,16L,16L),
G=c(14L,13L,5L),
T=c(10L,9L,13L)))
checkIdentical(alphabetFrequency(malign, collapse=TRUE)[1:4],
c(A=31L, C=46L, G=32L, T=32L))
}
test_DNAMultipleAlignment_named <- function()
{
malign <- make_DNAMultipleAlignment()
checkTrue(validObject(malign, test=TRUE))
checkIdentical(as.character(unmasked(malign)), strings_DNAMultipleAlignment())
checkIdentical(rownames(malign), names(strings_DNAMultipleAlignment()))
checkIdentical(rowmask(malign), new("NormalIRanges"))
checkIdentical(colmask(malign), new("NormalIRanges"))
checkIdentical(as.character(maskMotif(malign, "GC", fixed=FALSE)),
c(string1="AAGGTCTCCA-TCCTTCAGTGGAGTCATG--TCGGACA",
string2="AAGGTCTCCA-TCCTTCAGTGGAGTCATG--TCCGACA",
string3="CATTTATATATCCCTCCCCAAGAAACATAGTTTTGACA"))
checkIdentical(as.character(maskGaps(malign)),
strings_DNAMultipleAlignment())
checkIdentical(nrow(malign), length(strings_DNAMultipleAlignment()))
checkIdentical(ncol(malign), nchar(strings_DNAMultipleAlignment())[[1]])
checkIdentical(dim(malign),
c(length(strings_DNAMultipleAlignment()),
nchar(strings_DNAMultipleAlignment())[[1]]))
checkIdentical(maskednrow(malign), 0L)
checkIdentical(maskedncol(malign), 0L)
checkIdentical(maskeddim(malign), c(0L, 0L))
checkIdentical(maskedratio(malign), c(0, 0))
checkIdentical(nchar(malign), nchar(strings_DNAMultipleAlignment())[[1]])
checkIdentical(seqtype(malign), "DNA")
checkIdentical(as.character(malign), strings_DNAMultipleAlignment())
checkIdentical(consensusMatrix(malign)[1:4, 1:4],
rbind(A=c(2L,3L,0L,0L),
C=c(1L,0L,0L,0L),
G=c(0L,0L,2L,2L),
T=c(0L,0L,1L,1L)))
checkIdentical(consensusString(malign),
"MAKKTMTMYA-GSYYSCCCTYCMSYSWRGARRCRCWCATR--TYBGACA")
checkIdentical(as.character(consensusViews(malign)),
"MAKKTMTMYA-GSYYSCCCTYCMSYSWRGARRCRCWCATR--TYBGACA")
checkIdentical(alphabetFrequency(malign)[,1:4],
cbind(A=c(8L,8L,15L),
C=c(14L,16L,16L),
G=c(14L,13L,5L),
T=c(10L,9L,13L)))
checkIdentical(alphabetFrequency(malign, collapse=TRUE)[1:4],
c(A=31L, C=46L, G=32L, T=32L))
}
### FIXME!!
BROKEN_test_DNAMultipleAlignment_mask_some <- function()
{
malign <- make_DNAMultipleAlignment()
rowmask(malign) <- IRanges(2,2)
colmask(malign) <- IRanges(c(1,21,43), c(10,35,49))
checkTrue(validObject(malign, test=TRUE))
checkIdentical(as.character(unmasked(malign)), strings_DNAMultipleAlignment())
checkIdentical(rownames(malign), names(strings_DNAMultipleAlignment()))
checkIdentical(rowmask(malign), asNormalIRanges(IRanges(2,2)))
checkIdentical(colmask(malign), asNormalIRanges(IRanges(c(1,21,43), c(10,35,49))))
checkIdentical(as.character(maskMotif(malign, "GC", fixed=FALSE)),
c(string1="-TCCTTCATG--", string3="TCCCTACATAGT"))
checkIdentical(as.character(maskGaps(malign, min.block.width=1)),
c(string1="GCCTGCCCTTCATG", string3="GGTCCCCCTACATA"))
checkIdentical(nrow(malign), length(strings_DNAMultipleAlignment()))
checkIdentical(ncol(malign), nchar(strings_DNAMultipleAlignment())[[1]])
checkIdentical(dim(malign),
c(length(strings_DNAMultipleAlignment()),
nchar(strings_DNAMultipleAlignment())[[1]]))
checkIdentical(maskednrow(malign), 1L)
checkIdentical(maskedncol(malign), 32L)
checkIdentical(maskeddim(malign), c(1L, 32L))
checkIdentical(maskedratio(malign), c(1/3, 32/49))
checkIdentical(nchar(malign), 17L)
checkIdentical(seqtype(malign), "DNA")
checkIdentical(as.character(malign),
c(string1="-GCCTGCCCTTCATG--", string3="TGGTCCCCCTACATAGT"))
checkIdentical(consensusMatrix(malign)[1:4, 1:4],
rbind(A=rep(NA_integer_,4),
C=rep(NA_integer_,4),
G=rep(NA_integer_,4),
T=rep(NA_integer_,4)))
checkIdentical(consensusString(malign),
"##########TGSYYSCCCT###############WCATRGT#######")
checkIdentical(as.character(consensusViews(malign)),
c("TGSYYSCCCT", "WCATRGT"))
checkIdentical(alphabetFrequency(malign)[,1:4],
cbind(A=c(1L,NA,3L),
C=c(6L,NA,6L),
G=c(3L,NA,3L),
T=c(4L,NA,5L)))
checkIdentical(alphabetFrequency(malign, collapse=TRUE)[1:4],
c(A=4L, C=12L, G=6L, T=9L))
}
### FIXME!!
BROKEN_test_DNAMultipleAlignment_mask_all_rows <- function()
{
malign <- make_DNAMultipleAlignment()
rowmask(malign) <- IRanges(1,3)
colmask(malign) <- IRanges(c(1,21,43), c(10,35,49))
checkTrue(validObject(malign, test=TRUE))
checkIdentical(as.character(unmasked(malign)), strings_DNAMultipleAlignment())
checkIdentical(rownames(malign), names(strings_DNAMultipleAlignment()))
checkIdentical(rowmask(malign), asNormalIRanges(IRanges(1,3)))
checkIdentical(colmask(malign), asNormalIRanges(IRanges(c(1,21,43), c(10,35,49))))
checkIdentical(as.character(maskMotif(malign, "GC", fixed=FALSE)), character())
checkIdentical(as.character(maskGaps(malign)), character())
checkIdentical(nrow(malign), length(strings_DNAMultipleAlignment()))
checkIdentical(ncol(malign), nchar(strings_DNAMultipleAlignment())[[1]])
checkIdentical(dim(malign),
c(length(strings_DNAMultipleAlignment()),
nchar(strings_DNAMultipleAlignment())[[1]]))
checkIdentical(maskednrow(malign), 3L)
checkIdentical(maskedncol(malign), 32L)
checkIdentical(maskeddim(malign), c(3L, 32L))
checkIdentical(maskedratio(malign), c(3/3, 32/49))
checkIdentical(nchar(malign), 17L)
checkIdentical(seqtype(malign), "DNA")
checkIdentical(as.character(malign), character(0))
checkIdentical(consensusMatrix(malign)[1:4, 1:4],
rbind(A=rep(NA_integer_,4),
C=rep(NA_integer_,4),
G=rep(NA_integer_,4),
T=rep(NA_integer_,4)))
checkIdentical(consensusString(malign),
"#################################################")
checkIdentical(alphabetFrequency(malign)[,1:4],
cbind(A=rep(NA_integer_, 3),
C=rep(NA_integer_, 3),
G=rep(NA_integer_, 3),
T=rep(NA_integer_, 3)))
checkIdentical(alphabetFrequency(malign, collapse=TRUE)[1:4],
c(A=0L, C=0L, G=0L, T=0L))
}
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