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 = 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)

[Package AnnotationHubData version 1.20.2 Index]