download_fasta_intergenic {BgeeCall} | R Documentation

## 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')
    }

[Package BgeeCall version 1.3.1 Index]