XStringSet
s to artifacts and back againalabaster.string 1.4.0
The alabaster.string package implements methods to save XStringSet
objects to file artifacts and load them back into R.
Check out the alabaster.base for more details on the motivation and concepts of the alabaster framework.
Given an XStringSet
, we can use saveObject()
to save it inside a staging directory:
library(Biostrings)
x <- DNAStringSet(c(seq1="CTCNACCAGTAT", seq2="TTGA", seq3="TACCTAGAG"))
mcols(x)$score <- runif(length(x))
x
## DNAStringSet object of length 3:
## width seq names
## [1] 12 CTCNACCAGTAT seq1
## [2] 4 TTGA seq2
## [3] 9 TACCTAGAG seq3
library(alabaster.string)
tmp <- tempfile()
saveObject(x, tmp)
list.files(tmp, recursive=TRUE)
## [1] "OBJECT"
## [2] "names.txt.gz"
## [3] "sequence_annotations/OBJECT"
## [4] "sequence_annotations/basic_columns.h5"
## [5] "sequences.fasta.gz"
We can then load it back into the session with readObject()
.
roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "DNAStringSet"
## attr(,"package")
## [1] "Biostrings"
More details on the metadata and on-disk layout are provided in the schema.
The same approach works with QualityScaledXStringSet
objects:
x <- DNAStringSet(c("TTGA", "CTCN"))
q <- PhredQuality(c("*+,-", "6789"))
y <- QualityScaledDNAStringSet(x, q)
library(alabaster.string)
tmp <- tempfile()
saveObject(y, tmp)
roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "QualityScaledDNAStringSet"
## attr(,"package")
## [1] "Biostrings"
sessionInfo()
## R version 4.4.0 beta (2024-04-15 r86425 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows Server 2022 x64 (build 20348)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=C
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] alabaster.string_1.4.0 alabaster.base_1.4.0 Biostrings_2.72.0
## [4] GenomeInfoDb_1.40.0 XVector_0.44.0 IRanges_2.38.0
## [7] S4Vectors_0.42.0 BiocGenerics_0.50.0 BiocStyle_2.32.0
##
## loaded via a namespace (and not attached):
## [1] crayon_1.5.2 httr_1.4.7 cli_3.6.2
## [4] knitr_1.46 rlang_1.1.3 xfun_0.43
## [7] UCSC.utils_1.0.0 jsonlite_1.8.8 htmltools_0.5.8.1
## [10] sass_0.4.9 rmarkdown_2.26 evaluate_0.23
## [13] jquerylib_0.1.4 fastmap_1.1.1 Rhdf5lib_1.26.0
## [16] alabaster.schemas_1.4.0 yaml_2.3.8 lifecycle_1.0.4
## [19] bookdown_0.39 BiocManager_1.30.22 compiler_4.4.0
## [22] Rcpp_1.0.12 rhdf5filters_1.16.0 rhdf5_2.48.0
## [25] digest_0.6.35 R6_2.5.1 GenomeInfoDbData_1.2.12
## [28] bslib_0.7.0 tools_4.4.0 zlibbioc_1.50.0
## [31] cachem_1.0.8