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().
## Not run: 
# meta <- updateResources("/local/path", 
#                         BiocVersion = c("3.2", "3.3"),
#                         preparerClasses = "GencodeFastaImportPreparer",
#                         metadataOnly = TRUE, insert = FALSE,
#                         justRunUnitTest = FALSE)
# 
# ## End(Not run)