makeGencodeFasta: 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.sanger.ac.uk/pub/gencode/",
                      species=c("Human", "Mouse"), release, 
                      justRunUnitTest=FALSE, 
                      BiocVersion=biocVersion())
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.

Value

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

Details

Documentation:

{ http://www.gencodegenes.org/releases/ } File download location:{ ftp://ftp.sanger.ac.uk/pub/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(). }

Examples

Run this code

## 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().
meta <- updateResources("/local/path", 
                        BiocVersion = c("3.2", "3.3"),
                        preparerClasses = "GencodeFastaImportPreparer",
                        metadataOnly = TRUE, insert = FALSE,
                        justRunUnitTest = FALSE)