BSgenomeForge 1.2.1
BSgenome data packages are one of the many types of annotation packages available in Bioconductor. They contain the genomic sequences, which comprise chromosome sequences and other DNA sequences of a particular genome assembly for a given organism. For example BSgenome.Hsapiens.UCSC.hg19 is a BSgenome data package that contains the genomic sequences of the hg19 genome from UCSC. Users can easily and efficiently access the sequences, or portions of the sequences, stored in these packages, via a common API implemented in the BSgenome software package.
Bioconductor currently provides more than 100 BSgenome data packages, for more than 30 organisms. Most of them contain the genomic sequences of UCSC genomes (i.e. genomes supported by the UCSC Genome Browser) or NCBI assemblies. The packages are used in various Bioconductor workflows, as well as in man page examples and vignettes of other Bioconductor packages, typically in conjunction with tools available in the BSgenomeForge and Biostrings software packages. New BSgenome data packages get added on a regular basis, based on user demand.
The current process of forging a BSgenome data package requires one to download
the sequence data files, either as a single twoBit file (e.g. musFur1.2bit) or
in a collection of compressed FASTA files. The user then needs to prepare the
BSgenome data package seed file, and then call forgeBSgenomeDataPkg function
on the seed file to forge the package. This is quite a convoluted task that can
be an inconvenience for the average user.
The BSgenomeForge package simplifies the whole process, by allowing the user to
use one function to create a BSgenome data package. It is comprised of two main
functions: forgeBSgenomeDataPkgfromNCBI and forgeBSgenomeDataPkgfromUCSC
which allow the user to forge BSgenome data packages with sequence data files
sourced from NCBI or UCSC respectively.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BSgenomeForge")forgeBSgenomeDataPkgFromNCBI()library(BSgenomeForge)Example 1: Information about assembly ASM972954v1 can be found at https://www.ncbi.nlm.nih.gov/assembly/GCF_009729545.1/, including the assembly accession, GCA_009729545.1 and organism name, Acidianus infernus. Assembly ASM972954v1 does not contain any circular sequences to be specified:
forgeBSgenomeDataPkgFromNCBI(assembly_accession="GCA_009729545.1",
pkg_maintainer="Jane Doe <janedoe@gmail.com>",
organism="Acidianus infernus")## Creating package in ./BSgenome.Ainfernus.NCBI.ASM972954v1Example 2: Information about assembly ASM836960v1 can be found at https://www.ncbi.nlm.nih.gov/assembly/GCA_008369605.1/, including the assembly accession, GCA_008369605.1 and organism name, Vibrio cholerae. Assembly ASM836960v1 contains three circular sequence, “1”, “2” and “unnamed”. See CP043554.1, CP043556.1, and CP043555.1 in the NCBI Nucleotide database at https://www.ncbi.nlm.nih.gov/nuccore/. They must be specified as shown in the example below:
forgeBSgenomeDataPkgFromNCBI(assembly_accession="GCA_008369605.1",
pkg_maintainer="Jane Doe <janedoe@gmail.com>",
organism="Vibrio cholerae",
circ_seqs = c("1", "2", "unnamed"))## Creating package in ./BSgenome.Vcholerae.NCBI.ASM836960v1Check ?forgeBSgenomeDataPkgFromNCBI for more information.
forgeBSgenomeDataPkgFromUCSC()Example 3: Information about genome wuhCor1 can be found at https://genome.ucsc.edu/cgi-bin/hgGateway. This belongs to the organism Severe acute respiratory syndrome coronavirus 2. Genome wuhCor1 does not contain any circular sequences to be specified:
forgeBSgenomeDataPkgFromUCSC(
genome="wuhCor1",
organism="Severe acute respiratory syndrome coronavirus 2",
pkg_maintainer="Jane Doe <janedoe@gmail.com>"
)## Creating package in ./BSgenome.Scoronavirus2.UCSC.wuhCor1Check ?forgeBSgenomeDataPkgFromUCSC for more information.
forgeBSgenomeDataPkgfromNCBI or forgeBSgenomeDataPkgfromUCSC returns the
path to the created package at the end of its execution. This can be used to
find the package location, and afterwards carry out the following commands to
build the package source tarball via command line (i.e. in a Linux/Unix terminal
or Windows PowerShell terminal).
R CMD build <pkgdir>where <pkgdir> is the path to the source tree of the package. Then check the package with
R CMD check <tarball>where <tarball> is the path to the tarball produced by R CMD build. Finally install the package with
R CMD INSTALL <tarball>These operations can also be carried out within R, instead, using the devtools package
devtools::build("./BSgenome.Ainfernus.NCBI.ASM972954v1")## ── R CMD build ─────────────────────────────────────────────────────────────────
## * checking for file ‘/tmp/RtmpAr9uHK/Rbuilda878bf353df/BSgenomeForge/vignettes/BSgenome.Ainfernus.NCBI.ASM972954v1/DESCRIPTION’ ... OK
## * preparing ‘BSgenome.Ainfernus.NCBI.ASM972954v1’:
## * checking DESCRIPTION meta-information ... OK
## * checking for LF line-endings in source and make files and shell scripts
## * checking for empty or unneeded directories
## * building ‘BSgenome.Ainfernus.NCBI.ASM972954v1_1.0.0.tar.gz’## [1] "/tmp/RtmpAr9uHK/Rbuilda878bf353df/BSgenomeForge/vignettes/BSgenome.Ainfernus.NCBI.ASM972954v1_1.0.0.tar.gz"devtools::check_built("BSgenome.Ainfernus.NCBI.ASM972954v1_1.0.0.tar.gz")devtools::install_local("BSgenome.Ainfernus.NCBI.ASM972954v1_1.0.0.tar.gz")sessionInfo()## R version 4.3.2 Patched (2023-11-13 r85521)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] BSgenomeForge_1.2.1 BSgenome_1.70.1 rtracklayer_1.62.0
## [4] BiocIO_1.12.0 GenomicRanges_1.54.1 Biostrings_2.70.1
## [7] XVector_0.42.0 GenomeInfoDb_1.38.5 IRanges_2.36.0
## [10] S4Vectors_0.40.2 BiocGenerics_0.48.1 BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-7 fastmap_1.1.1
## [3] RCurl_1.98-1.13 GenomicAlignments_1.38.0
## [5] promises_1.2.1 XML_3.99-0.16
## [7] digest_0.6.33 mime_0.12
## [9] lifecycle_1.0.4 ellipsis_0.3.2
## [11] processx_3.8.3 magrittr_2.0.3
## [13] compiler_4.3.2 rlang_1.1.2
## [15] sass_0.4.8 tools_4.3.2
## [17] yaml_2.3.8 knitr_1.45
## [19] S4Arrays_1.2.0 htmlwidgets_1.6.4
## [21] pkgbuild_1.4.3 DelayedArray_0.28.0
## [23] pkgload_1.3.3 abind_1.4-5
## [25] BiocParallel_1.36.0 miniUI_0.1.1.1
## [27] purrr_1.0.2 desc_1.4.3
## [29] grid_4.3.2 urlchecker_1.0.1
## [31] profvis_0.3.8 xtable_1.8-4
## [33] SummarizedExperiment_1.32.0 cli_3.6.2
## [35] rmarkdown_2.25 crayon_1.5.2
## [37] remotes_2.4.2.1 rstudioapi_0.15.0
## [39] rjson_0.2.21 sessioninfo_1.2.2
## [41] cachem_1.0.8 stringr_1.5.1
## [43] zlibbioc_1.48.0 parallel_4.3.2
## [45] BiocManager_1.30.22 restfulr_0.0.15
## [47] matrixStats_1.2.0 vctrs_0.6.5
## [49] devtools_2.4.5 Matrix_1.6-4
## [51] jsonlite_1.8.8 bookdown_0.37
## [53] callr_3.7.3 jquerylib_0.1.4
## [55] glue_1.6.2 codetools_0.2-19
## [57] ps_1.7.5 stringi_1.8.3
## [59] later_1.3.2 htmltools_0.5.7
## [61] GenomeInfoDbData_1.2.11 R6_2.5.1
## [63] evaluate_0.23 shiny_1.8.0
## [65] lattice_0.22-5 Biobase_2.62.0
## [67] Rsamtools_2.18.0 memoise_2.0.1
## [69] httpuv_1.6.13 bslib_0.6.1
## [71] Rcpp_1.0.11 SparseArray_1.2.3
## [73] xfun_0.41 fs_1.6.3
## [75] MatrixGenerics_1.14.0 usethis_2.2.2