makeGencodeFasta {AnnotationHubData} | R Documentation

## Recipe to add Gencode FASTA resources to AnnotationHub

### Description

Create metadata and process raw Gencode FASTA files for inclusion in AnnotationHub

### Usage

    makeGencodeFastaToAHM(currentMetadata,
                          baseUrl="ftp://ftp.ebi.ac.uk/pub/databases/gencode/",
                          species=c("Human", "Mouse"), release,
                          justRunUnitTest=FALSE,
                          BiocVersion=BiocManager::version())

    gencodeFastaToFaFile(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.
`species` | A `character(1)` of the species. Currently "Human" and "Mouse" are supported.
`release` | A `character` string of the release number.
`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

- Documentation: http://www.gencodegenes.org/releases/

- File download location: ftp://ftp.ebi.ac.uk/pub/databases/gencode/. Gencode_human and Gencode_mouse are used.

- Files downloaded: Code is currently specific for human and mouse. Files chosen for download are described in AnnotationHubData:::.gencodeDescription().

### Value

`makeGencodeFastaAHM` returns a list of `AnnotationHubMetadata` instances. `gencodeFastaToFaFile` returns nothing.

### Author(s)

Bioconductor Core Team.

### See Also

- updateResources

- AnnotationHubMetadata

### Examples

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

    ## To run the GencodeFasta recipe specify
    ## 'preparerClasses = GencodeFastaImportPreparer'. The 'species' and 'release'
    ## arguments are passed to makeGencodeFastaAHM().
    ## Not run:
    meta <- updateResources("/local/path",
                            BiocVersion = c("3.2", "3.3"),
                            preparerClasses = "GencodeFastaImportPreparer",
                            metadataOnly = TRUE, insert = FALSE,
                            justRunUnitTest = FALSE)

    ## End(Not run)

[Package AnnotationHubData version 1.18.1 Index]