Ref

Retrieves reference files from the Ensembl FTP site.

Help

Name	Short	Long	Description
Species	`-s`	`--species`	Species to query data for [default: homo_sapiens]
Release	`-r`	`--release`	Release to use - will default to latest release
Data Type	`-d`	`--datatype`	Datatype to query for - provided as a comma-separated list
Output	`-o`	`--output`	optional filepath to write output to [default=stdout]
Download	`-D`	`--download`	Download all requested files to the current working directory

Command Line Interface

# returns the url for human genome (default)
ggetrs ensembl ref

# returns the url for the human cdna transcriptome
ggetrs ensembl ref -d cdna

# returns the url for the human cdna transcriptome and genome
ggetrs ensembl ref -d cdna,dna

# returns the url for the mouse cdna transcriptome and genome
ggetrs ensembl ref -d cdna,dna -s mus_musculus

# downloads the requested files to the current directory
ggetrs ensembl ref -d cdna,dna,gtf -s homo_sapiens

Python

import ggetrs

# returns the url for human genome (default)
ggetrs.ensembl.reference()

# returns the url for the human cdna transcriptome
ggetrs.ensembl.reference(
  datatype="cdna"
)

# returns the url for the human cdna transcriptome and genome
ggetrs.ensembl.reference(
  datatype=["cdna", "dna"]
)

# returns the url for the mouse cdna transcriptome and genome
ggetrs.ensembl.reference(
  datatype=["cdna", "dna"], 
  species="mus_musculus"
)