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 info 💡

Fetch extensive gene and transcript metadata from Ensembl, UniProt, and NCBI using Ensembl IDs.
Return format: JSON (command-line) or data frame/CSV (Python).

Positional argument
ens_ids
One or more Ensembl IDs.

Optional arguments
-o --out
Path to the file 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
-n --ncbi
TURN OFF results from NCBI.
Python: ncbi=False prevents data retrieval from NCBI (default: True).

-u --uniprot
TURN OFF results from UniProt.
Python: uniprot=False prevents data retrieval from UniProt (default: True).

-pdb --pdb
INCLUDE PDB IDs in output (might increase runtime).
Python: pdb=True includes PDB IDs in the results (default: False).

-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 info ENSG00000034713 ENSG00000104853 ENSG00000170296

# Python
gget.info(["ENSG00000034713", "ENSG00000104853", "ENSG00000170296"])

→ Returns extensive information about each requested Ensembl ID:

More examples