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

makeEnsemblFasta {AnnotationHubData}

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/", release,
                      justRunUnitTest = FALSE, BiocVersion = biocVersion())

makeEnsemblTwoBitToAHM(currentMetadata, baseUrl = "ftp://ftp.ensembl.org/pub/",
                       baseDir = "fasta/", release,
                       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.
`release`	Integer version number, e.g., "84".
`justRunUnitTest`	A `logical`. When TRUE, a small number of records (usually 5) are processed instead of all.
`BiocVersion`	A `character(1)` Bioconductor version. The resource will be available in Bioconductor >= to this version. Default value is the current version, specified with biocVersion().
`ahm`	List of `AnnotationHubMetadata` instances.

Details

makeEnsemblFastaToAHM and makeEnsemblTwoBitToAHM process metadata into a list of AnnotationHubMetadata objects.

ensemblFastaToFaFile unzips a .gz files, creates and index and writes out .rz and .rz.fai files to disk. ensemblFastaToTwoBit converts a fasta file to twobit format and writes the .2bit file out to disk.

Value

makeEnsemblFastaToAHM and makeEnsemblTwoBitToAHM return a list of AnnotationHubMetadata objects.

ensemblFastaToFaFile write out .rz and .rz.fai files to disk. ensemblFastaToTwoBit writes out a .2bit file to disk.

Author(s)

Bioconductor Core Team

Examples

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

## 'release' is passed to makeEnsemblFastaToFaFile.
## Not run: 
meta <- updateResources("/local/path", 
                        BiocVersion = c("3.2", "3.3"),
                        preparerClasses = "EnsemblFastaImportPreparer",
                        metadataOnly = TRUE, insert = FALSE,
                        justRunUnitTest = FALSE, release = "83")

## End(Not run)

[Package AnnotationHubData version 1.8.1 Index]