Species

Returns the available species in the Ensembl FTP site

Arguments

Name	Short	Long	Description
Release	`-r`	`--release`	Ensembl release version to use - will default to latest release
Data Type	`-d`	`--datatype`	Datatype to query species list [default: dna] [possible values: cdna, cds, dna, gff3, gtf, ncrna, pep]
Output	`-o`	`--output`	optional filepath to write output to [default=stdout]

Command Line Interface

# return all species where there is a genome (i.e. dna)
ggetrs ensembl species

# return all species where there is a transcriptome (i.e. cdna)
ggetrs ensembl species -d cdna

# return all species where there is a transcriptome (i.e. cdna)
# for an older release
ggetrs ensembl species -d cdna -r 60

Python

import ggetrs

# return all species where there is a genome (i.e. dna)
ggetrs.ensembl.species()

# return all species where there is a transcriptome (i.e. cdna)
ggetrs.ensembl.species(dataype="dna")

# return all species where there is a transcriptome (i.e. cdna)
# for an older release
ggetrs.ensembl.species(dataype="cdna", release=60)