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BSgenomeForge

The BSgenomeForge functions

Description

A set of functions for making a BSgenome data package.

Usage

## Top-level BSgenomeForge function:

forgeBSgenomeDataPkg(x, seqs_srcdir=".", destdir=".", verbose=TRUE)

## Low-level BSgenomeForge functions:

forgeSeqlengthsRdsFile(seqnames, prefix="", suffix=".fa",
                       seqs_srcdir=".", seqs_destdir=".",
                       genome=NA_character_, verbose=TRUE)

forgeSeqlengthsRdaFile(seqnames, prefix="", suffix=".fa",
                       seqs_srcdir=".", seqs_destdir=".",
                       genome=NA_character_, verbose=TRUE)

forgeSeqFiles(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)

forgeMasksFiles(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)

Arguments

x

A BSgenomeDataPkgSeed object or the name of a BSgenome data package seed file. See the BSgenomeForge vignette in this package for more information.

seqs_srcdir, masks_srcdir

Single strings indicating the path to the source directories i.e. to the directories containing the source data files. Only read access to these directories is needed. See the BSgenomeForge vignette in this package for more information.

destdir

A single string indicating the path to the directory where the source tree of the target package should be created. This directory must already exist. See the BSgenomeForge vignette in this package for more information.

verbose

TRUE or FALSE.

provider

The provider of the sequence data files e.g. "UCSC", "NCBI", "BDGP", "FlyBase", etc...

genome

The name of the genome. Typically the name of an NCBI assembly (e.g. "GRCh38.p12", "WBcel235", "TAIR10.1", "ARS-UCD1.2", etc...) or UCSC genome (e.g. "hg38", "bosTau9", "galGal6", "ce11", etc...).

seqnames, mseqnames

A character vector containing the names of the single (for seqnames) and multiple (for mseqnames) sequences to forge. See the BSgenomeForge vignette in this package for more information.

seqfile_name, prefix, suffix

See the BSgenomeForge vignette in this package for more information, in particular the description of the seqfile_name, seqfiles_prefix and seqfiles_suffix fields of a BSgenome data package seed file.

seqs_destdir, masks_destdir

During the forging process the source data files are converted into serialized Biostrings objects. seqs_destdir and masks_destdir must be single strings indicating the path to the directories where these serialized objects should be saved. These directories must already exist.

Both forgeSeqlengthsRdsFile and forgeSeqlengthsRdaFile will produce a single .rds or .rda file. Both forgeSeqFiles and forgeMasksFiles will produce one file per sequence (all files being either .rds or .rda files).

ondisk_seq_format

Specifies how the single sequences should be stored in the forged package. Can be "2bit", "rds", "rda", "fa.rz", or "fa". If "2bit" (the default), then all the single sequences are stored in a single twoBit file. If "rds" or "rda", then each single sequence is stored in a separated serialized XString derivative (one per single sequence). If "fa.rz" or "fa", then all the single sequences are stored in a single FASTA file (compressed in the RAZip format if "fa.rz").

nmask_per_seq

A single integer indicating the desired number of masks per sequence. See the BSgenomeForge vignette in this package for more information.

AGAPSfiles_type, AGAPSfiles_name, AGAPSfiles_prefix, AGAPSfiles_suffix, RMfiles_name, RMfiles_prefix, RMfiles_suffix, TRFfiles_name, TRFfiles_prefix, TRFfiles_suffix

These arguments are named accordingly to the corresponding fields of a BSgenome data package seed file. See the BSgenomeForge vignette in this package for more information.

Details

These functions are intended for Bioconductor users who want to make a new BSgenome data package, not for regular users of these packages. See the BSgenomeForge vignette in this package (vignette("BSgenomeForge")) for an extensive coverage of this topic.

Author(s)

H. Pagès

Examples

seqs_srcdir <- system.file("extdata", package="BSgenome")
seqnames <- c("chrX", "chrM")

## Forge .2bit sequence files:
forgeSeqFiles("UCSC", "ce2",
              seqnames, prefix="ce2", suffix=".fa.gz",
              seqs_srcdir=seqs_srcdir,
              seqs_destdir=tempdir(), ondisk_seq_format="2bit")

## Forge .rds sequence files:
forgeSeqFiles("UCSC", "ce2",
              seqnames, prefix="ce2", suffix=".fa.gz",
              seqs_srcdir=seqs_srcdir,
              seqs_destdir=tempdir(), ondisk_seq_format="rds")

## Sanity checks:
library(BSgenome.Celegans.UCSC.ce2)
genome <- BSgenome.Celegans.UCSC.ce2

ce2_sequences <- import(file.path(tempdir(), "single_sequences.2bit"))
ce2_sequences0 <- DNAStringSet(list(chrX=genome$chrX, chrM=genome$chrM))
stopifnot(identical(names(ce2_sequences0), names(ce2_sequences)),
          all(ce2_sequences0 == ce2_sequences))

chrX <- readRDS(file.path(tempdir(), "chrX.rds"))
stopifnot(genome$chrX == chrX)
chrM <- readRDS(file.path(tempdir(), "chrM.rds"))
stopifnot(genome$chrM == chrM)
BSgenome

Software infrastructure for efficient representation of full genomes and their SNPs

v1.58.0
Artistic-2.0
Authors
Hervé Pagès
Initial release

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