GitHub - ArtifactDB/alabaster.string: Save and load XStringSets from file

Save biological sequence data to file

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"