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

Description Usage Arguments Details Value Author(s) See Also Examples

Description

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

Usage

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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

See Also

Examples

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## 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. 24, 2018, 9:22 a.m.