makeGencodeFasta: Recipe to add Gencode FASTA resources to AnnotationHub

In AnnotationHubData: Transform public data resources into Bioconductor Data Structures

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)

AnnotationHubData documentation built on April 17, 2021, 6:05 p.m.