gget

Python arguments are equivalent to long-option arguments (--arg), unless otherwise specified. Flags are True/False arguments in Python. The manual for any gget tool can be called from the command-line using the -h --help flag.

gget search 🔎

Fetch genes and transcripts from Ensembl using free-form search terms.
Results are matched based on the "gene name" and "description" sections in the Ensembl database. gget version >= 0.27.9 also includes results that match the Ensembl "synonym" section.
Return format: JSON (command-line) or data frame/CSV (Python).

Positional argument
searchwords
One or more free form search words, e.g. gaba nmda. (Note: Search is not case-sensitive.)

Other required arguments
-s --species
Species or database to be searched.
A species can be passed in the format 'genus_species', e.g. 'homo_sapiens' or 'arabidopsis_thaliana'.
To pass a specific database, pass the name of the CORE database, e.g. 'mus_musculus_dba2j_core_105_1'.

All available core databases can be found here:
Vertebrates: http://ftp.ensembl.org/pub/current/mysql/
Invertebrates: http://ftp.ensemblgenomes.org/pub/current/ + select kingdom + go to mysql/

Supported shortcuts: 'human', 'mouse'

Optional arguments
-r --release
Defines the Ensembl release number from which the files are fetched, e.g. 104. Default: None -> latest Ensembl release is used.
Note: Does not apply to invertebrate species (you can pass a specific core database (which includes a release number) to the species argument instead).
This argument is overwritten if a specific database (which includes a release number) is passed to the species argument.

-t --id_type
'gene' (default) or 'transcript'
Returns genes or transcripts, respectively.

-ao --andor
'or' (default) or 'and'
'or': Returns all genes that INCLUDE AT LEAST ONE of the searchwords in their name/description.
'and': Returns only genes that INCLUDE ALL of the searchwords in their name/description.

-l --limit
Limits the number of search results, e.g. 10. Default: None.

-o --out
Path to the csv the results will be saved in, e.g. path/to/directory/results.csv (or .json). Default: Standard out.
Python: save=True will save the output in the current working directory.

Flags
-csv --csv
Command-line only. Returns results in CSV format.
Python: Use json=True to return output in JSON format.

-q --quiet
Command-line only. Prevents progress information from being displayed.
Python: Use verbose=False to prevent progress information from being displayed.

wrap_text
Python only. wrap_text=True displays data frame with wrapped text for easy reading (default: False).

Example

gget search -s human gaba gamma-aminobutyric

# Python
gget.search(["gaba", "gamma-aminobutyric"], "homo_sapiens")

→ Returns all genes that contain at least one of the search words in their name or Ensembl/external reference description:

More examples