makeGencodeFasta: Recipe to add Gencode FASTA resources to AnnotationHub

In Bioconductor/AnnotationHubData: Transform public data resources into Bioconductor Data Structures

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)

Bioconductor/AnnotationHubData documentation built on Oct. 31, 2024, 8:13 a.m.