makeEnsemblFasta: Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.

Description

Transform an Ensembl FASTA file to a Bioconductor FaFile or ToBitFile.

Usage

makeEnsemblFastaToAHM(currentMetadata, baseUrl = "ftp://ftp.ensembl.org/pub/",
                      baseDir = "fasta/", regex,
                      justRunUnitTest = FALSE, BiocVersion = biocVersion())
makeEnsemblTwoBitToAHM(currentMetadata, baseUrl = "ftp://ftp.ensembl.org/pub/",
                       baseDir = "fasta/", regex,
                       justRunUnitTest = FALSE, BiocVersion = biocVersion())
ensemblFastaToFaFile(ahm)
ensemblFastaToTwoBitFile(ahm)

Arguments

currentMetadata

Currently not used. Intended to be a list of metadata to filter, i.e., records that do not need to be processed again. Need to remove or fix.

baseUrl

ftp file location.

baseDir

ftp file directory.

regex

Regular expression to match release version, e.g., "*.release-81".

justRunUnitTest

A logical. When TRUE, a small number of records (usually 5) are processed instead of all.

BiocVersion

A character vector of Bioconductor versions the resources should be available for.

ahm

List of AnnotationHubMetadata instances.

Value

TODO

Details

TODO

Examples

Run this code

## updateResources() generates metadata, process records and
## pushes files to AWS S3 buckets. See ?updateResources for details.

## 'regex' is passed to makeEnsemblFastaToFaFile.
meta <- updateResources("/local/path", 
                        BiocVersion = c("3.2", "3.3"),
                        preparerClasses = "EnsemblFastaImportPreparer",
                        metadataOnly = TRUE, insert = FALSE,
                        justRunUnitTest = FALSE, regex = ".*release-82")