| Environment | Status |
|---|---|
| BioC-release |  |
| BioC-devel |  |
The alabaster.string package implements methods for saving and loading XStringSet objects under the alabaster framework.
It provides a language-agnostic method for serializing biological sequences along with any sequence-specific metadata.
To get started, install the package and its dependencies from Bioconductor:
# install.packages("BiocManager")
BiocManager::install("alabaster.string")In the example below, we save a QualityScaledDNAStringSet object to file:
library(Biostrings)
example(QualityScaledDNAStringSet, echo=FALSE) # can't be bothered to copy it here.
qdna1
## A QualityScaledDNAStringSet instance containing:
##
## DNAStringSet object of length 2:
## width seq
## [1] 4 TTGA
## [2] 4 CTCN
##
## PhredQuality object of length 2:
## width seq
## [1] 4 *+,-
## [2] 4 6789
library(alabaster.string)
tmp <- tempfile()
saveObject(qdna1, tmp)
roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "QualityScaledDNAStringSet"
## attr(,"package")
## [1] "Biostrings"