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BSgenomeForge.R
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BSgenomeForge.R
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### =========================================================================
### The BSgenomeForge functions
### -------------------------------------------------------------------------
.getMasksObjname <- function(seqnames)
{
if (length(seqnames) == 0)
return(character(0))
paste0(seqnames, ".masks")
}
.saveObjectToRdsFile <- function(object, objname, destdir=".", verbose=TRUE)
{
destfile <- file.path(destdir, paste0(objname, ".rds"))
if (verbose)
cat("Saving '", objname, "' object to compressed data file '",
destfile, "' ... ", sep="")
## Using compress="xz" (instead of compress="gzip") would produce a .rds
## file that is about 20% smaller on disk but it would also take almost 3x
## longer to load it later on with load(). Tested on hg19 chr1 with R-2.14
## (2011-09-20 r57033). This is why we stick to compress="gzip".
saveRDS(object, file=destfile, compress="gzip")
if (verbose)
cat("DONE\n")
}
.saveObjectToRdaFile <- function(object, objname, destdir=".", verbose=TRUE)
{
assign(objname, object)
destfile <- file.path(destdir, paste0(objname, ".rda"))
if (verbose)
cat("Saving '", objname, "' object to compressed data file '",
destfile, "' ... ", sep="")
## Using compress="xz" (instead of compress="gzip") would produce a .rda
## file that is about 20% smaller on disk but it would also take almost 3x
## longer to load it later on with load(). Tested on hg19 chr1 with R-2.14
## (2011-09-20 r57033). This is why we stick to compress="gzip".
save(list=objname, file=destfile, compress="gzip")
if (verbose)
cat("DONE\n")
remove(list=objname)
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### The "getSeqSrcpaths" function.
###
getSeqSrcpaths <- function(seqnames, prefix="", suffix=".fa", seqs_srcdir=".")
{
if (!is.null(seqnames) && !is.character(seqnames))
stop("'seqnames' must be a character vector (or NULL)")
if (length(seqnames) == 0L) {
warning("'seqnames' is empty")
return(setNames(character(0), character(0)))
}
if (!isSingleString(prefix))
stop("'prefix' must be a single string")
if (!isSingleString(suffix))
stop("'suffix' must be a single string")
if (!isSingleString(seqs_srcdir))
stop("'seqs_srcdir' must be a single string")
srcfiles <- paste0(prefix, seqnames, suffix)
ans <- file.path(seqs_srcdir, srcfiles)
is_OK <- file.exists(ans)
if (!all(is_OK)) {
files_not_found <- paste(ans[!is_OK], collapse=", ")
stop("file(s) not found: ", files_not_found)
}
names(ans) <- seqnames
ans
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### getSeqlengths(), forgeSeqlengthsRdsFile(), and forgeSeqlengthsRdaFile()
###
getSeqlengths <- function(seqnames, prefix="", suffix=".fa", seqs_srcdir=".",
genome=NA_character_)
{
srcpaths <- getSeqSrcpaths(seqnames, prefix=prefix, suffix=suffix,
seqs_srcdir=seqs_srcdir)
ans <- vapply(setNames(seq_along(seqnames), seqnames),
function(i) {
seqname <- seqnames[[i]]
srcpath <- srcpaths[[seqname]]
ans <- fasta.seqlengths(srcpath)
if (i %% 200L == 0L) {
## Unfortunately, the files opened by fasta.seqlengths() only
## get closed at garbage collection time! So if we don't
## explicitly call gc() every once in a while in this loop,
## we run into the risk of reaching the maximum number of
## files that can be opened simultaneously on the system (this
## is OS-dependent). This is a huge drawback of using
## XVector::open_input_files() internally to open the files!
gc()
}
if (length(ans) == 0L)
stop("In file '", srcpath, "': no sequence found")
if (length(ans) > 1L)
warning("In file '", srcpath, "': ", length(ans),
" sequences found, using first sequence only")
if (names(ans)[[1L]] != seqname)
warning("In file '", srcpath, "': sequence description \"",
names(ans), "\" doesn't match user-specified ",
"sequence name \"", seqname, "\"")
ans[[1L]]
},
integer(1),
USE.NAMES=TRUE
)
if (!is.na(genome)) {
expected <- seqlengths(Seqinfo(genome=genome))
if (!identical(expected[names(ans)], ans))
stop("the sequences in the files have lengths that don't match ",
"the lengths reported by 'Seqinfo(genome=\"", genome, "\")'")
}
ans
}
forgeSeqlengthsRdsFile <- function(seqnames, prefix="", suffix=".fa",
seqs_srcdir=".", seqs_destdir=".",
genome=NA_character_, verbose=TRUE)
{
if (!isSingleString(seqs_destdir))
stop("'seqs_destdir' must be a single string")
seqlengths <- getSeqlengths(seqnames, prefix=prefix, suffix=suffix,
seqs_srcdir=seqs_srcdir, genome=genome)
.saveObjectToRdsFile(seqlengths, "seqlengths", destdir=seqs_destdir,
verbose=verbose)
}
forgeSeqlengthsRdaFile <- function(seqnames, prefix="", suffix=".fa",
seqs_srcdir=".", seqs_destdir=".",
genome=NA_character_, verbose=TRUE)
{
if (!isSingleString(seqs_destdir))
stop("'seqs_destdir' must be a single string")
seqlengths <- getSeqlengths(seqnames, prefix=prefix, suffix=suffix,
seqs_srcdir=seqs_srcdir, genome=genome)
.saveObjectToRdaFile(seqlengths, "seqlengths", destdir=seqs_destdir,
verbose=verbose)
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### forgeSeqFiles()
###
.forgeRdsSeqFile <- function(name, prefix, suffix, seqs_srcdir, seqs_destdir,
is.single.seq=TRUE, verbose=TRUE)
{
if (!isSingleString(name))
stop("'name' must be a single string")
srcpath <- getSeqSrcpaths(name, prefix=prefix, suffix=suffix,
seqs_srcdir=seqs_srcdir)
if (verbose)
cat("Loading FASTA file '", srcpath, "' ... ", sep="")
seq <- readDNAStringSet(srcpath, "fasta")
if (verbose)
cat("DONE\n")
if (is.single.seq) {
if (length(seq) == 0L)
stop("file contains no DNA sequence")
if (length(seq) > 1L)
warning("file contains ", length(seq), " sequences, ",
"using the first sequence only")
seq <- seq[[1L]] # now 'seq' is a DNAString object
}
.saveObjectToRdsFile(seq, name, destdir=seqs_destdir, verbose=verbose)
}
.forgeRdaSeqFile <- function(name, prefix, suffix, seqs_srcdir, seqs_destdir,
is.single.seq=TRUE, verbose=TRUE)
{
if (!isSingleString(name))
stop("'name' must be a single string")
srcpath <- getSeqSrcpaths(name, prefix=prefix, suffix=suffix,
seqs_srcdir=seqs_srcdir)
if (verbose)
cat("Loading FASTA file '", srcpath, "' in '", name,
"' object ... ", sep="")
seq <- readDNAStringSet(srcpath, "fasta")
if (verbose)
cat("DONE\n")
if (is.single.seq) {
if (length(seq) == 0L)
stop("file contains no DNA sequence")
if (length(seq) > 1L)
warning("file contains ", length(seq), " sequences, ",
"using the first sequence only")
seq <- seq[[1]] # now 'seq' is a DNAString object
}
.saveObjectToRdaFile(seq, name, destdir=seqs_destdir, verbose=verbose)
}
.forgeFastaRzFileFromFastaFiles <- function(seqnames, prefix, suffix,
seqs_srcdir, seqs_destdir,
ondisk_seq_format, verbose=TRUE)
{
if (!is.character(seqnames))
stop("'seqnames' must be a character vector")
dest_filename <- "single_sequences.fa"
dest_filepath <- file.path(seqs_destdir, dest_filename)
for (seqname in seqnames) {
srcpath <- getSeqSrcpaths(seqname, prefix=prefix, suffix=suffix,
seqs_srcdir=seqs_srcdir)
if (verbose)
cat("Loading '", seqname, "' sequence from FASTA file '",
srcpath, "' ... ", sep="")
seq <- readDNAStringSet(srcpath, "fasta")
if (verbose)
cat("DONE\n")
if (length(seq) == 0L)
stop("file contains no DNA sequence")
if (length(seq) > 1L) {
warning("file contains ", length(seq), " sequences, ",
"using the first sequence only")
seq <- seq[1L]
}
if (verbose)
cat("Appending '", seqname, "' sequence to FASTA file '",
dest_filepath, "' ... ", sep="")
names(seq) <- seqname
writeXStringSet(seq, dest_filepath, append=TRUE,
format="fasta", width=50L)
if (verbose)
cat("DONE\n")
}
## Create the index.
if (ondisk_seq_format == "fa") {
## "fa" format
if (verbose)
cat("Indexing FASTA file '", dest_filepath, "' ... ", sep="")
indexFa(dest_filepath)
if (verbose)
cat("DONE\n")
} else {
## "fa.rz" format
if (verbose)
cat("Compressing FASTA file '", dest_filepath, "' ... ", sep="")
farz_filepath <- sprintf("%s.rz", dest_filepath)
razip(dest_filepath, dest=farz_filepath)
unlink(dest_filepath)
if (verbose)
cat("DONE\n")
if (verbose)
cat("Indexing compressed FASTA file '", farz_filepath,
"' ... ", sep="")
indexFa(farz_filepath)
if (verbose)
cat("DONE\n")
}
}
.replace_non_ACGTN_with_N <- function(x)
{
af <- alphabetFrequency(x)
non_ACGTN <- setdiff(names(af), c(DNA_BASES, "N"))
if (sum(af[non_ACGTN]) == 0L)
return(x)
warning(wmsg("DNA sequence contains letters not supported by UCSC 2bit ",
"format (the format\n only supports A, C, G, T, and N). ",
"Replacing them with Ns."))
old <- paste(non_ACGTN, collapse="")
new <- paste(rep.int("N", length(non_ACGTN)), collapse="")
chartr(old, new, x)
}
.forgeTwobitFileFromFastaFiles <- function(seqnames, prefix, suffix,
seqs_srcdir, seqs_destdir,
verbose=TRUE)
{
if (!is.character(seqnames))
stop("'seqnames' must be a character vector")
dest_filename <- "single_sequences.2bit"
dest_filepath <- file.path(seqs_destdir, dest_filename)
seqs <- setNames(vector(mode="list", length=length(seqnames)), seqnames)
for (seqname in seqnames) {
srcpath <- getSeqSrcpaths(seqname, prefix=prefix, suffix=suffix,
seqs_srcdir=seqs_srcdir)
if (verbose)
cat("Loading '", seqname, "' sequence from FASTA file '",
srcpath, "' ... ", sep="")
seq <- readDNAStringSet(srcpath, "fasta")
if (verbose)
cat("DONE\n")
if (length(seq) == 0L)
stop("file contains no DNA sequence")
if (length(seq) > 1L) {
warning("file contains ", length(seq), " sequences, ",
"using the first sequence only")
seq <- seq[1L]
}
seq <- .replace_non_ACGTN_with_N(seq[[1L]])
seqs[[seqname]] <- seq
}
seqs <- DNAStringSet(seqs)
if (verbose)
cat("Writing all sequences to '", dest_filepath, "' ... ", sep="")
export(seqs, dest_filepath, format="2bit")
if (verbose)
cat("DONE\n")
}
.subsetTwobitFile <- function(seqfile_name, seqnames,
seqs_srcdir, seqs_destdir,
verbose=verbose)
{
src_filepath <- file.path(seqs_srcdir, seqfile_name)
dest_filename <- "single_sequences.2bit"
dest_filepath <- file.path(seqs_destdir, dest_filename)
if (verbose)
cat("Loading '", src_filepath, "' ... ", sep="")
seqs <- import(src_filepath)
if (verbose)
cat("DONE\n")
idx <- match(seqnames, names(seqs))
notfound_idx <- which(is.na(idx))
if (length(notfound_idx) != 0L)
stop("sequence(s) not found: ",
paste(seqnames[notfound_idx], collapse=", "))
seqs <- seqs[idx]
if (verbose)
cat("Writing sequences to '", dest_filepath, "' ... ", sep="")
export(seqs, dest_filepath, format="2bit")
if (verbose)
cat("DONE\n")
}
.copyTwobitFile <- function(seqfile_name,
seqs_srcdir, seqs_destdir,
verbose=TRUE)
{
src_filepath <- file.path(seqs_srcdir, seqfile_name)
if (!file.exists(src_filepath))
stop("File not found: ", src_filepath)
dest_filename <- "single_sequences.2bit"
dest_filepath <- file.path(seqs_destdir, dest_filename)
if (verbose)
cat("Copying '", src_filepath, "' to '", dest_filepath, "' ... ",
sep="")
if (!file.copy(src_filepath, dest_filepath,
copy.mode=FALSE, copy.date=FALSE)) {
if (verbose)
stop("FAILED")
stop("Failed to copy '", src_filepath, "' to '", dest_filepath, "'")
}
if (verbose)
cat("DONE\n")
}
.sortUCSCTwobitFile <- function(genome, seqs_dir, verbose=TRUE)
{
if (verbose)
cat("Getting chrom info from UCSC with 'getChromInfoFromUCSC(\"",
genome, "\")' ... ", sep="")
chrom_info <- getChromInfoFromUCSC(genome)
if (verbose)
cat("DONE\n")
filename <- "single_sequences.2bit"
filepath <- file.path(seqs_dir, filename)
if (verbose)
cat("Loading '", filepath, "' ... ", sep="")
seqs <- import(filepath)
if (verbose)
cat("DONE\n")
m <- match(chrom_info[ , "chrom"], names(seqs))
if (nrow(chrom_info) != length(seqs) || anyNA(m))
stop(wmsg("nb of sequences in 'chromInfo' table and 2bit file ",
"don't match for UCSC genome ", genome))
if (verbose)
cat("Sorting sequences as in 'getChromInfoFromUCSC(\"",
genome, "\")' ... ", sep="")
seqs <- seqs[m]
if (verbose)
cat("DONE\n")
if (verbose)
cat("Checking the sequence lengths ... ")
if (!identical(chrom_info[ , "size"], width(seqs)))
stop(wmsg("sequence lengths in 'chromInfo' table and 2bit file ",
"don't match for UCSC genome ", genome))
if (verbose)
cat("OK\n")
if (verbose)
cat("Writing sequences to '", filepath, "' ... ", sep="")
export(seqs, filepath, format="2bit")
if (verbose)
cat("DONE\n")
}
forgeSeqFiles <- function(provider, genome,
seqnames, mseqnames=NULL,
seqfile_name=NA, prefix="", suffix=".fa",
seqs_srcdir=".", seqs_destdir=".",
ondisk_seq_format=c("2bit", "rds", "rda", "fa.rz", "fa"),
verbose=TRUE)
{
if (length(seqnames) == 0L && is.na(seqfile_name))
warning("'seqnames' is empty")
if (!(length(mseqnames) == 0L || is.character(mseqnames)))
stop("'mseqnames' must be a character vector (or NULL)")
if (!isSingleString(seqs_destdir))
stop("'seqs_destdir' must be a single string")
ondisk_seq_format <- match.arg(ondisk_seq_format)
if (ondisk_seq_format == "rds") { # "rds" format
for (name in seqnames) {
.forgeRdsSeqFile(name, prefix, suffix, seqs_srcdir, seqs_destdir,
is.single.seq=TRUE, verbose=verbose)
}
} else if (ondisk_seq_format == "rda") { # "rda" format
for (name in seqnames) {
.forgeRdaSeqFile(name, prefix, suffix, seqs_srcdir, seqs_destdir,
is.single.seq=TRUE, verbose=verbose)
}
} else if (ondisk_seq_format == "2bit") { # "2bit" format
if (is.na(seqfile_name)) {
.forgeTwobitFileFromFastaFiles(seqnames, prefix, suffix,
seqs_srcdir, seqs_destdir,
verbose=verbose)
} else if (length(seqnames) != 0L) {
.subsetTwobitFile(seqfile_name, seqnames,
seqs_srcdir, seqs_destdir,
verbose=verbose)
} else {
.copyTwobitFile(seqfile_name,
seqs_srcdir, seqs_destdir,
verbose=verbose)
if (provider == "UCSC") {
UCSC_genomes <- registered_UCSC_genomes()
if (genome %in% UCSC_genomes[ , "genome"])
.sortUCSCTwobitFile(genome, seqs_destdir,
verbose=verbose)
}
}
} else { # "fa" and "fa.rz" formats
.forgeFastaRzFileFromFastaFiles(seqnames, prefix, suffix,
seqs_srcdir, seqs_destdir,
ondisk_seq_format, verbose=verbose)
}
for (name in mseqnames) {
.forgeRdaSeqFile(name, prefix, suffix, seqs_srcdir, seqs_destdir,
is.single.seq=FALSE, verbose=verbose)
}
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### .copy_CITATION_file()
###
.copy_CITATION_file <- function(citation_file, pkgdir, verbose=TRUE)
{
if (!file.exists(citation_file))
stop("File not found: ", citation_file)
dest_filename <- "CITATION"
dest_filepath <- file.path(pkgdir, "inst", dest_filename)
if (verbose)
cat("Copying '", citation_file, "' to '", dest_filepath, "' ... ",
sep="")
if (!file.copy(citation_file, dest_filepath,
copy.mode=FALSE, copy.date=FALSE)) {
if (verbose)
stop("FAILED")
stop("Failed to copy '", citation_file, "' to '", dest_filepath, "'")
}
if (verbose)
cat("DONE\n")
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### forgeMasksFiles()
###
## AGAPS is the mask of "assembly gaps" (inter-contig Ns).
## If 'filetype' is:
## NA: then AGAPS is an empty mask;
## "gap": then AGAPS is extracted from a UCSC "gap" file;
## "agp": then AGAPS is extracted from an NCBI "agp" file.
## AGAPS is active by default.
.forge.AGAPSmask <- function(seqname, mask_width, masks_srcdir,
filetype, filename,
fileprefix, filesuffix)
{
if (!isSingleStringOrNA(filetype))
stop("'filetype' must be a single string or NA")
if (!isSingleStringOrNA(filename))
stop("'filename' must be a single string or NA")
if (!isSingleStringOrNA(fileprefix))
stop("'fileprefix' must be a single string or NA")
if (!isSingleStringOrNA(filesuffix))
stop("'filesuffix' must be a single string or NA")
if (is.na(filetype)) {
ans <- Mask(mask_width)
desc(ans) <- "assembly gaps (empty)"
} else {
if (is.na(filename))
filename <- paste0(fileprefix, seqname, filesuffix)
filepath <- file.path(masks_srcdir, filename)
if (filetype == "gap")
ans <- read.gapMask(filepath, seqname=seqname, mask.width=mask_width)
else
ans <- read.agpMask(filepath, seqname=seqname, mask.width=mask_width)
}
active(ans) <- TRUE
names(ans) <- "AGAPS"
ans
}
## AMB is the mask of "intra-contig ambiguities".
## AMB is active by default.
.forge.AMBmask <- function(seq, AGAPSmask)
{
active(AGAPSmask) <- TRUE
masks(seq) <- AGAPSmask
amb_letters <- names(IUPAC_CODE_MAP)[nchar(IUPAC_CODE_MAP) > 1]
for (amb_letter in amb_letters)
seq <- maskMotif(seq, amb_letter)
ans <- collapse(masks(seq)[-1])
desc(ans) <- "intra-contig ambiguities"
if (isEmpty(ans))
desc(ans) <- paste0(desc(ans), " (empty)")
active(ans) <- TRUE
names(ans) <- "AMB"
ans
}
## RM is the "RepeatMasker" mask (from the RepeatMasker .out file).
## RM is NOT active by default.
.forge.RMmask <- function(seqname, mask_width, masks_srcdir,
filename, fileprefix, filesuffix)
{
if (!isSingleStringOrNA(filename))
stop("'filename' must be a single string or NA")
if (!isSingleStringOrNA(fileprefix))
stop("'fileprefix' must be a single string or NA")
if (!isSingleStringOrNA(filesuffix))
stop("'filesuffix' must be a single string or NA")
if (is.na(filename))
filename <- paste0(fileprefix, seqname, filesuffix)
filepath <- file.path(masks_srcdir, filename)
if (file.exists(filepath)) {
ans <- read.rmMask(filepath, seqname=seqname, mask.width=mask_width)
desc(ans) <- "RepeatMasker"
} else {
ans <- Mask(mask_width)
desc(ans) <- "RepeatMasker (empty)"
}
active(ans) <- FALSE
names(ans) <- "RM"
ans
}
## TRF is the "Tandem Repeats Finder" mask (from the Tandem Repeats Finder
## .bed file).
## TRF is NOT active by default.
.forge.TRFmask <- function(seqname, mask_width, masks_srcdir,
filename, fileprefix, filesuffix)
{
if (!isSingleStringOrNA(filename))
stop("'filename' must be a single string or NA")
if (!isSingleStringOrNA(fileprefix))
stop("'fileprefix' must be a single string or NA")
if (!isSingleStringOrNA(filesuffix))
stop("'filesuffix' must be a single string or NA")
if (is.na(filename))
filename <- paste0(fileprefix, seqname, filesuffix)
filepath <- file.path(masks_srcdir, filename)
if (file.exists(filepath)) {
ans <- read.trfMask(filepath, seqname=seqname, mask.width=mask_width)
desc(ans) <- "Tandem Repeats Finder [period<=12]"
} else {
ans <- Mask(mask_width)
desc(ans) <- "Tandem Repeats Finder [period<=12] (empty)"
}
active(ans) <- FALSE
names(ans) <- "TRF"
ans
}
.forgeMasksFile <- function(seqname, nmask_per_seq,
seqs_destdir=".",
ondisk_seq_format=c("2bit", "rda", "fa.rz", "fa"),
masks_srcdir=".", masks_destdir=".",
AGAPSfiles_type="gap", AGAPSfiles_name=NA,
AGAPSfiles_prefix="", AGAPSfiles_suffix="_gap.txt",
RMfiles_name=NA, RMfiles_prefix="", RMfiles_suffix=".fa.out",
TRFfiles_name=NA, TRFfiles_prefix="", TRFfiles_suffix=".bed",
verbose=TRUE)
{
if (!isSingleString(seqname))
stop("'seqname' must be a single string")
if (!is.numeric(nmask_per_seq)
|| length(nmask_per_seq) != 1
|| !(nmask_per_seq %in% 0:4))
stop("'nmask_per_seq' must be 0, 1, 2, 3 or 4")
if (nmask_per_seq == 0)
warning("forging an empty mask collection ('nmask_per_seq' is set to 0)")
if (!isSingleString(seqs_destdir))
stop("'seqs_destdir' must be a single string")
if (!isSingleString(masks_srcdir))
stop("'masks_srcdir' must be a single string")
if (!isSingleString(masks_destdir))
stop("'masks_destdir' must be a single string")
## Load the sequence.
ondisk_seq_format <- match.arg(ondisk_seq_format)
if (ondisk_seq_format == "rda") { # "rda" format
seqfile <- file.path(seqs_destdir, paste0(seqname, ".rda"))
load(seqfile)
seq <- get(seqname)
remove(list=seqname)
} else if (ondisk_seq_format == "2bit") { # "2bit" format
twobit_filename <- "single_sequences.2bit"
twobit_filepath <- file.path(seqs_destdir, twobit_filename)
twobitfile <- TwoBitFile(twobit_filepath)
which <- GRanges(seqname, IRanges(1L, seqlengths(twobitfile)[[seqname]]))
seq <- import(twobitfile, which=which)[[1L]]
} else { # "fa" and "fa.rz" formats
fa_filename <- "single_sequences.fa"
if (ondisk_seq_format == "fa.rz")
fa_filename <- paste0(fa_filename, ".rz")
fa_filepath <- file.path(seqs_destdir, fa_filename)
fafile <- FaFile(fa_filepath)
## TODO: Implement "[[" method for FaFile objects (in Rsamtools) and
## use it here (i.e. do 'seq <- fafile[[seqname]]' instead of the 2
## lines below).
param <- GRanges(seqname, IRanges(1L, seqlengths(fafile)[[seqname]]))
seq <- scanFa(fafile, param=param)[[1L]]
}
mask_width <- length(seq)
## Start with an empty mask collection (i.e. a MaskCollection of
## length 0).
masks <- new("MaskCollection", width=mask_width)
if (nmask_per_seq >= 1) {
AGAPSmask <- .forge.AGAPSmask(seqname, mask_width, masks_srcdir,
AGAPSfiles_type, AGAPSfiles_name,
AGAPSfiles_prefix, AGAPSfiles_suffix)
masks <- append(masks, AGAPSmask)
}
if (nmask_per_seq >= 2) {
AMBmask <- .forge.AMBmask(seq, AGAPSmask)
masks <- append(masks, AMBmask)
}
if (nmask_per_seq >= 3) {
RMmask <- .forge.RMmask(seqname, mask_width, masks_srcdir,
RMfiles_name, RMfiles_prefix, RMfiles_suffix)
masks <- append(masks, RMmask)
}
if (nmask_per_seq >= 4) {
TRFmask <- .forge.TRFmask(seqname, mask_width, masks_srcdir,
TRFfiles_name, TRFfiles_prefix, TRFfiles_suffix)
masks <- append(masks, TRFmask)
}
objname <- .getMasksObjname(seqname)
.saveObjectToRdaFile(masks, objname, destdir=masks_destdir, verbose=verbose)
}
forgeMasksFiles <- function(seqnames, nmask_per_seq,
seqs_destdir=".",
ondisk_seq_format=c("2bit", "rda", "fa.rz", "fa"),
masks_srcdir=".", masks_destdir=".",
AGAPSfiles_type="gap", AGAPSfiles_name=NA,
AGAPSfiles_prefix="", AGAPSfiles_suffix="_gap.txt",
RMfiles_name=NA, RMfiles_prefix="", RMfiles_suffix=".fa.out",
TRFfiles_name=NA, TRFfiles_prefix="", TRFfiles_suffix=".bed",
verbose=TRUE)
{
if (length(seqnames) == 0L)
warning("'seqnames' is empty")
for (seqname in seqnames) {
.forgeMasksFile(seqname, nmask_per_seq,
seqs_destdir=seqs_destdir,
ondisk_seq_format=ondisk_seq_format,
masks_srcdir=masks_srcdir, masks_destdir=masks_destdir,
AGAPSfiles_type=AGAPSfiles_type, AGAPSfiles_name=AGAPSfiles_name,
AGAPSfiles_prefix=AGAPSfiles_prefix, AGAPSfiles_suffix=AGAPSfiles_suffix,
RMfiles_name=RMfiles_name, RMfiles_prefix=RMfiles_prefix, RMfiles_suffix=RMfiles_suffix,
TRFfiles_name=TRFfiles_name, TRFfiles_prefix=TRFfiles_prefix, TRFfiles_suffix=TRFfiles_suffix,
verbose=verbose)
}
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### The BSgenomeDataPkgSeed and MaskedBSgenomeDataPkgSeed classes and their
### low-level constructors.
###
setClass("BSgenomeDataPkgSeed",
representation(
Package="character",
Title="character",
Description="character",
Version="character",
Author="character",
Maintainer="character",
Suggests="character",
License="character",
organism="character",
common_name="character",
## Should be accepted by 'Seqinfo(genome=genome)' e.g. "TAIR10.1",
## "hg38", "ce11" etc...
genome="character",
provider="character",
provider_version="character", # deprecated in favor of 'genome'
release_date="character",
release_name="character", # deprecated (not replaced by anything)
source_url="character",
organism_biocview="character",
BSgenomeObjname="character",
seqnames="character", # a single string containing R source code
circ_seqs="character", # a single string containing R source code
mseqnames="character", # a single string containing R source code
PkgDetails="character",
SrcDataFiles="character",
PkgExamples="character",
seqfile_name="character",
seqfiles_prefix="character",
seqfiles_suffix="character",
ondisk_seq_format="character",
citation_file="character" # a single string containing R source code
),
prototype(
Author="The Bioconductor Dev Team",
Maintainer="Bioconductor Package Maintainer <maintainer@bioconductor.org>",
Suggests="",
License="Artistic-2.0",
genome=NA_character_,
provider_version=NA_character_,
release_name=NA_character_,
source_url="-- information not available --",
seqnames=NA_character_,
circ_seqs=NA_character_,
mseqnames="NULL", # equivalent to "character(0)"
PkgDetails="",
SrcDataFiles="-- information not available --",
PkgExamples="",
seqfile_name=NA_character_,
seqfiles_prefix="",
seqfiles_suffix=".fa",
ondisk_seq_format="2bit",
citation_file=NA_character_
)
)
setClass("MaskedBSgenomeDataPkgSeed",
representation(
Package="character",
Title="character",
Description="character",
Version="character",
Author="character",
Maintainer="character",
RefPkgname="character",
Suggests="character",
License="character",
source_url="character",
organism_biocview="character",
nmask_per_seq="integer", # a single integer
PkgDetails="character",
SrcDataFiles="character",
PkgExamples="character",
AGAPSfiles_type="character",
AGAPSfiles_name="character",
AGAPSfiles_prefix="character",
AGAPSfiles_suffix="character",
RMfiles_name="character",
RMfiles_prefix="character",
RMfiles_suffix="character",
TRFfiles_name="character",
TRFfiles_prefix="character",
TRFfiles_suffix="character"
),
prototype(
Author="The Bioconductor Dev Team",
Maintainer="Bioconductor Package Maintainer <maintainer@bioconductor.org>",
Suggests="",
License="Artistic-2.0",
source_url="-- information not available --",
nmask_per_seq=0L,
PkgDetails="",
SrcDataFiles="-- information not available --",
PkgExamples="",
AGAPSfiles_type="gap",
AGAPSfiles_name=as.character(NA),
AGAPSfiles_prefix="",
AGAPSfiles_suffix="_gap.txt",
RMfiles_name=as.character(NA),
RMfiles_prefix="",
RMfiles_suffix=".fa.out",
TRFfiles_name=as.character(NA),
TRFfiles_prefix="",
TRFfiles_suffix=".bed"
)
)
### Generic transformation of a named list into an S4 object with automatic
### coercion of the list elements to the required types.
makeS4FromList <- function(Class, x)
{
if (!is.list(x) || is.null(names(x)))
stop("'x' must be a named list")
explicit_slots <- getSlots(Class)[names(x)]
if (any(is.na(explicit_slots))) {
invalid_names <- setdiff(names(x), names(getSlots(Class)))
stop("some names in 'x' are not valid ", Class, " slots (",
paste(invalid_names, collapse=", "), ")")
}
y <- lapply(seq_len(length(x)),
function(i) {
x_elt <- x[[i]]
if (is(x_elt, explicit_slots[i]))
return(x_elt)
as(x_elt, explicit_slots[i])
})
names(y) <- names(x)
y$Class <- Class
do.call(new, y)
}
BSgenomeDataPkgSeed <- function(x)
makeS4FromList("BSgenomeDataPkgSeed", x)
MaskedBSgenomeDataPkgSeed <- function(x)
makeS4FromList("MaskedBSgenomeDataPkgSeed", x)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### The "forgeBSgenomeDataPkg" generic and methods.
###
setGeneric("forgeBSgenomeDataPkg", signature="x",
function(x, seqs_srcdir=".", destdir=".", replace=FALSE, verbose=TRUE)
standardGeneric("forgeBSgenomeDataPkg")
)
setMethod("forgeBSgenomeDataPkg", "BSgenomeDataPkgSeed",
function(x, seqs_srcdir=".", destdir=".", replace=FALSE, verbose=TRUE)
{
if (!isTRUEorFALSE(replace))
stop("'replace' must be TRUE or FALSE")
## The Biobase package is needed for createPackage().
if (!requireNamespace("Biobase", quietly=TRUE))
stop("Couldn't load the Biobase package. Please install ",
"the Biobase\n package and try again.")
template_path <- system.file("pkgtemplates", "BSgenome_datapkg",
package="BSgenome")
BSgenome_version <- installed.packages()['BSgenome','Version']
if (is.na(x@genome)) {
if (is.na(x@provider_version))
stop("'genome' field is missing in seed file")
warning("field 'provider_version' is deprecated ",
"in favor of 'genome'")
x@genome <- x@provider_version
}
if (!is.na(x@release_name))
warning("field 'release_name' is deprecated")
seqnames <- x@seqnames
if (!is.na(seqnames)) {
.seqnames <- eval(parse(text=seqnames))
} else {
if (is.na(x@seqfile_name)) {
.seqnames <- seqlevels(Seqinfo(genome=x@genome))
} else {
.seqnames <- NULL
}
}
seqnames <- deparse1(.seqnames)
circ_seqs <- x@circ_seqs
if (!is.na(circ_seqs)) {
.circ_seqs <- eval(parse(text=circ_seqs))
} else {
si <- Seqinfo(genome=x@genome)
.circ_seqs <- seqlevels(si)[isCircular(si)]
}
circ_seqs <- deparse1(.circ_seqs)
symvals <- list(
PKGTITLE=x@Title,
PKGDESCRIPTION=x@Description,
PKGVERSION=x@Version,
AUTHOR=x@Author,
MAINTAINER=x@Maintainer,
BSGENOMEVERSION=BSgenome_version,
SUGGESTS=x@Suggests,
LICENSE=x@License,
ORGANISM=x@organism,
COMMONNAME=x@common_name,
GENOME=x@genome,
PROVIDER=x@provider,
RELEASEDATE=x@release_date,
SOURCEURL=x@source_url,
ORGANISMBIOCVIEW=x@organism_biocview,
BSGENOMEOBJNAME=x@BSgenomeObjname,
SEQNAMES=seqnames,
CIRCSEQS=circ_seqs,
MSEQNAMES=x@mseqnames,
PKGDETAILS=x@PkgDetails,
SRCDATAFILES=x@SrcDataFiles,
PKGEXAMPLES=x@PkgExamples
)
## Should never happen
if (any(duplicated(names(symvals)))) {
str(symvals)
stop("'symvals' contains duplicated symbols")
}
## All symvals should by single strings (non-NA)
is_OK <- sapply(symvals, isSingleString)
if (!all(is_OK)) {
bad_syms <- paste(names(is_OK)[!is_OK], collapse=", ")
stop("values for symbols ", bad_syms, " are not single strings")
}
pkgdir <- file.path(destdir, x@Package)
if (file.exists(pkgdir)) {
if (replace) {
unlink(pkgdir, recursive=TRUE)
} else {
stop("directory ", pkgdir, " exists. ",
"Use replace=TRUE to replace it.")
}
}
Biobase::createPackage(x@Package, destdir, template_path, symvals)
.mseqnames <- eval(parse(text=x@mseqnames))
seqs_destdir <- file.path(pkgdir, "inst", "extdata")
if (x@ondisk_seq_format == "rds") {
## Forge the "seqlengths.rds" file
forgeSeqlengthsRdsFile(.seqnames,
prefix=x@seqfiles_prefix,
suffix=x@seqfiles_suffix,
seqs_srcdir=seqs_srcdir,
seqs_destdir=seqs_destdir,
genome=x@genome,
verbose=verbose)
} else if (x@ondisk_seq_format == "rda") {
## Forge the "seqlengths.rda" file
forgeSeqlengthsRdaFile(.seqnames,
prefix=x@seqfiles_prefix,
suffix=x@seqfiles_suffix,
seqs_srcdir=seqs_srcdir,
seqs_destdir=seqs_destdir,
genome=x@genome,
verbose=verbose)
}
## Forge the sequence files (either "2bit", "rds", "rda", "fa.rz",
## or "fa").
forgeSeqFiles(x@provider, x@genome,
.seqnames, mseqnames=.mseqnames,
seqfile_name=x@seqfile_name,
prefix=x@seqfiles_prefix,
suffix=x@seqfiles_suffix,
seqs_srcdir=seqs_srcdir,
seqs_destdir=seqs_destdir,
ondisk_seq_format=x@ondisk_seq_format,
verbose=verbose)
if (!is.na(x@citation_file)) {
citation_file <- eval(parse(text=x@citation_file))
.copy_CITATION_file(citation_file, pkgdir, verbose=verbose)
}
}
)
setMethod("forgeBSgenomeDataPkg", "list",
function(x, seqs_srcdir=".", destdir=".", replace=FALSE, verbose=TRUE)
{
y <- BSgenomeDataPkgSeed(x)
forgeBSgenomeDataPkg(y, seqs_srcdir=seqs_srcdir, destdir=destdir,
replace=replace, verbose=verbose)
}
)
.removeCommentLines <- function(infile=stdin(), outfile=stdout())
{
if (is.character(infile)) {
infile <- file(infile, "r")
on.exit(close(infile))
}
if (is.character(outfile)) {
outfile <- file(outfile, "w")
on.exit({close(infile); close(outfile)})
}
while (TRUE) {
lines <- readLines(infile, n=25000L)
if (length(lines) == 0L)
return()
keep_it <- substr(lines, 1L, 1L) != "#"
writeLines(lines[keep_it], outfile)
}
}
### A "comment aware" version of read.dcf().
read.dcf2 <- function(file, ...)
{
clean_file <- tempfile()