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### =========================================================================
### predictCoding methods
### =========================================================================
setMethod("predictCoding", c("IntegerRanges", "TxDb", "ANY", "DNAStringSet"),
function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE)
{
callGeneric(as(query, "GRanges"), subject, seqSource, varAllele, ...,
ignore.strand=ignore.strand)
})
setMethod("predictCoding", c("CollapsedVCF", "TxDb", "ANY", "missing"),
function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE)
{
rd <- rowRanges(query)
alt <- alt(query)
if (is(alt, "CharacterList")) {
alt <- .toDNAStringSetList(alt)
if (sum(elementNROWS(alt)) == 0L) {
stop("No nucleotide ALT values were detected.")
}
}
rd <- rep(rowRanges(query), elementNROWS(alt))
res <- callGeneric(rd, subject, seqSource, unlist(alt, use.names=FALSE),
..., ignore.strand=ignore.strand)
## adjust QUERYID for expansion of rowRanges
res$QUERYID <- rep(seq_len(length(alt)),
elementNROWS(alt))[res$QUERYID]
res
})
setMethod("predictCoding", c("ExpandedVCF", "TxDb", "ANY", "missing"),
function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE)
{
if (is(alt(query), "CharacterList")) {
stop("alt(query) must be a DNAStringSet (not a CharacterList)")
}
callGeneric(rowRanges(query), subject, seqSource, alt(query), ...,
ignore.strand=ignore.strand)
})
setMethod("predictCoding", c("GRanges", "TxDb", "ANY", "DNAStringSet"),
function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE)
{
.predictCoding(query, subject, seqSource, varAllele, ...,
ignore.strand=ignore.strand)
})
setMethod("predictCoding", c("VRanges", "TxDb", "ANY", "missing"),
function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE)
{
varAllele <- alt(query)
query <- as(query, "GRanges")
if (!is(varAllele, "DNAStringSet")) {
tryCatch({
varAllele <- DNAStringSet(varAllele)
}, error=function(e) {
stop(paste0("attempt to coerce 'alt' to DNAStringSet failed with ",
"error: ", conditionMessage(e)))
})
}
.predictCoding(query, subject, seqSource, varAllele, ...,
ignore.strand=ignore.strand)
})
.predictCoding <-
function(query, subject, seqSource, varAllele, ...,
cache=new.env(parent=emptyenv()), ignore.strand=FALSE)
{
stopifnot(length(varAllele) == length(query))
if (!any(seqlevels(query) %in% seqlevels(subject)))
warning("none of seqlevels(query) match seqlevels(subject)")
if (!exists(".__init__", cache, inherits=FALSE)) {
cache[["cdsbytx"]] <- cdsBy(subject)
cache[["txbygene"]] <- transcriptsBy(subject, "gene")
cache[[".__init__"]] <- TRUE
}
map <- data.frame(geneid=rep(names(cache[["txbygene"]]),
elementNROWS(cache[["txbygene"]])),
txid=mcols(unlist(cache[["txbygene"]],
use.names=FALSE))[["tx_id"]],
stringsAsFactors=FALSE)
txlocal <- .predictCodingGRangesList(query, cache[["cdsbytx"]],
seqSource, varAllele, ..., ignore.strand=ignore.strand)
txid <- mcols(txlocal)$TXID
mcols(txlocal)$GENEID <- map$geneid[match(txid, map$txid)]
txlocal
}
.predictCodingGRangesList <- function(query, cdsbytx, seqSource, varAllele,
..., genetic.code=GENETIC_CODE,
if.fuzzy.codon="error",
ignore.strand=FALSE)
{
if (ignore.strand)
strand(query) <- "*"
## variant location in cds region
mcols(query) <- append(mcols(query), DataFrame(varAllele=varAllele))
txlocal <- .localCoordinates(query, cdsbytx, ignore.strand=FALSE, ...)
if (length(txlocal) == 0)
return(txlocal)
## reverse complement "-" strand
valid <- rep(TRUE, length(txlocal))
nstrand <- as.vector(strand(txlocal) == "-")
if (any(nstrand)) {
va <- mcols(txlocal)$varAllele
va[nstrand] <- reverseComplement(va[valid & nstrand])
mcols(txlocal)$varAllele <- va
}
## frameshift
refwidth <- width(txlocal)
altallele <- mcols(txlocal)$varAllele
fmshift <- abs(width(altallele) - refwidth) %% 3 != 0
if (any(fmshift))
valid[fmshift] <- FALSE
## zero-width
zwidth <- width(altallele) == 0
if (any(zwidth)) {
warning("records with missing 'varAllele' were ignored")
valid[zwidth] <- FALSE
fmshift[zwidth] <- FALSE
}
## reference codon sequences
altpos <- (start(mcols(txlocal)$CDSLOC) - 1L) %% 3L + 1L
refCodon <- varCodon <- .getRefCodons(txlocal, altpos, seqSource, cdsbytx)
## allowed characters that can't be translated
## "N", ".", "+" and "-"
pattern <- "N|\\.|\\+|\\-"
altCheck <- grepl(pattern, as.character(altallele, use.names=FALSE))
refCheck <- grepl(pattern, as.character(refCodon, use.names=FALSE))
noTrans <- rep(FALSE, length(txlocal))
noTrans[altCheck | refCheck] <- TRUE
valid[noTrans] <- FALSE
if (any(altCheck))
warning("'varAllele' values with 'N', '.', '+' or '-'",
" were not translated")
if (any(refCheck))
warning("reference codons with 'N', '.', '+' or '-'",
" were not translated")
## substitute and translate
refAA <- varAA <- AAStringSet(rep("", length(txlocal)))
if (any(valid)) {
## 2 genetic.code versions
alt.init.codons <- attr(genetic.code, "alt_init_codons")
gc <- genetic.code
gc.no.alt.init.codons <- genetic.code
attr(gc.no.alt.init.codons, "alt_init_codons") <- character()
## ignore alt_init_codons
subseq(varCodon, altpos, width=refwidth) <- altallele
refAA[valid] <- translate(refCodon[valid],
genetic.code=gc.no.alt.init.codons,
if.fuzzy.codon=if.fuzzy.codon)
varAA <- AAStringSet(rep("", length(txlocal)))
varAA[valid] <- translate(varCodon[valid],
genetic.code=gc.no.alt.init.codons,
if.fuzzy.codon=if.fuzzy.codon)
## respect alt_init_codons at the start of the CDS
cds.start <- start(txlocal$CDSLOC) == 1L
varAA.to.modify <- varCodon %in% alt.init.codons & cds.start
refAA.to.modify <- refCodon %in% alt.init.codons & cds.start
if (any(cds.start)) {
varAA[varCodon %in% alt.init.codons & cds.start] <- "M"
refAA[refCodon %in% alt.init.codons & cds.start] <- "M"
}
}
## results
nonsynonymous <- as.character(refAA) != as.character(varAA)
consequence <- rep("synonymous", length(txlocal))
consequence[nonsynonymous] <- "nonsynonymous"
consequence[fmshift] <- "frameshift"
consequence[nonsynonymous & (as.character(varAA) %in% "*")] <- "nonsense"
consequence[zwidth | noTrans] <- "not translated"
consequence <- factor(consequence)
mcols(txlocal) <- append(mcols(txlocal),
DataFrame(GENEID=NA_character_,
CONSEQUENCE=consequence,
REFCODON=refCodon,
VARCODON=varCodon,
REFAA=refAA, VARAA=varAA))
txlocal
}
.getRefCodons <- function(txlocal, altpos, seqSource, cdsbytx)
{
## adjust codon end for
## - width of the reference sequence
## - position of alt allele substitution in the codon
cstart <- ((start(mcols(txlocal)$CDSLOC) - 1L) %/% 3L) * 3L + 1L
cend <- cstart + (((altpos + width(txlocal) - 2L) %/% 3L) * 3L + 2L)
txord <- match(mcols(txlocal)$TXID, names(cdsbytx))
txseqs <- extractTranscriptSeqs(seqSource, cdsbytx[txord])
DNAStringSet(substring(txseqs, cstart, cend))
}
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