download_fasta_intergenic: Download fasta intergenic

In BgeeDB/BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation

Download fasta intergenic

Description

Check if reference intergenic fasta file has already been downloaded. If not the file is downloaded from Bgee FTP or from the community repository depending on myBgeeMetadata@intergenic_release. if myBgeeMetadata@intergenic_release == "community" then reference intergenic wil be downloaded from the Zenodo community repository. Otherwise Reference intergenic sequences will be downloaded from the official Bgee FTP. Be careful when using reference intergenic sequences generated by the community as the Bgee team do not deeply review them.

Usage

download_fasta_intergenic(
  myBgeeMetadata = new("BgeeMetadata"),
  myUserMetadata,
  intergenic_file
)

Arguments

myBgeeMetadata	A Reference Class BgeeMetadata object (optional)
myUserMetadata	A Reference Class UserMetadata object.
intergenic_file	path where intergenic file will be saved

Value

download fasta intergenic from Bgee FTP or from the Zenodo community and save it locally

Examples

{
bgee_intergenic_file <- file.path(getwd(), 'intergenic.fasta')
userMetadata <- new('UserMetadata', species_id = '7227')
}

BgeeDB/BgeeCall documentation built on Nov. 10, 2023, 5:40 a.m.