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

In Bioconductor/AnnotationHubData: Transform public data resources into Bioconductor Data Structures

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 = BiocManager::version())

makeEnsemblTwoBitToAHM(currentMetadata, baseUrl = "ftp://ftp.ensembl.org/pub/",
                       baseDir = "fasta/", release,
                       justRunUnitTest = FALSE,
                       BiocVersion = BiocManager::version())

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 BiocManager::version().
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

See Also

• updateResources

• AnnotationHubMetadata

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)

Bioconductor/AnnotationHubData documentation built on Feb. 15, 2024, 10:10 a.m.