R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Functions to convert Ensembl FASTA files to FaFile and...

makeEnsemblFasta

R Documentation

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.

Details

TODO

Value

TODO

Author(s)

Bioconductor Core Team

Examples

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

## 'regex' is passed to makeEnsemblFastaToFaFile.
## Not run: 
meta <- updateResources("/local/path", 
                        BiocVersion = c("3.2", "3.3"),
                        preparerClasses = "EnsemblFastaImportPreparer",
                        metadataOnly = TRUE, insert = FALSE,
                        justRunUnitTest = FALSE, regex = ".*release-82")

## End(Not run)