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 cosmic 🪐

Search for genes, mutations, and other factors associated with cancer using the COSMIC (Catalogue Of Somatic Mutations In Cancer) database.
Return format: JSON (command-line) or data frame/CSV (Python) when download_cosmic=False. When download_cosmic=True, downloads the requested database into the specified folder.

This module was written in part by @AubakirovArman (information querying) and @josephrich98 (database download).

NOTE: License fees apply for the commercial use of COSMIC. You can read more about licensing COSMIC data here.

Positional argument (for querying information)
searchterm
Search term, which can be a mutation, or gene name (or Ensembl ID), or sample, etc.
Examples for the searchterm and entitity arguments:

NOTE: (Python only) Set to None when downloading COSMIC databases with download_cosmic=True.

Optional arguments (for querying information)
-e --entity
'mutations' (default), 'genes', 'cancer', 'tumour site', 'studies', 'pubmed', or 'samples'.
Defines the type of the results to return.

-l --limit
Limits number of hits to return. Default: 100.

Flags (for downloading COSMIC databases)
-d --download_cosmic
Switches into database download mode.

-gm --gget_mutate
TURNS OFF creation of a modified version of the database for use with gget mutate.
Python: gget_mutate is True by default. Set gget_mutate=False to disable.

Optional arguments (for downloading COSMIC databases)
-mc --mutation_class
'cancer' (default), 'cell_line', 'census', 'resistance', 'genome_screen', 'targeted_screen', or 'cancer_example'
Type of COSMIC database to download.

-cv --cosmic_version
Version of the COSMIC database. Default: None -> Defaults to latest version.

-gv --grch_version
Version of the human GRCh reference genome the COSMIC database was based on (37 or 38). Default: 37

--keep_genome_info Whether to keep genome information in the modified database for use with gget mutate. Default: False

--remove_duplicates Whether to remove duplicate rows from the modified database for use with gget mutate. Default: False

Optional arguments (general)
-o --out
Path to the file (or folder when downloading databases with the download_cosmic flag) the results will be saved in, e.g. 'path/to/results.json'.
Default: None
-> When download_cosmic=False: Results will be returned to standard out
-> When download_cosmic=True: Database will be downloaded into current working directory

Flags (general)
-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.

Examples

Query information

gget cosmic EGFR

# Python
gget.cosmic("EGFR")

→ Returns mutations in the EGFR gene that are associated with cancer in the format:

Downloading COSMIC databases

gget cosmic --download_cosmic

# Python
gget.cosmic(searchterm=None, download_cosmic=True)

→ Downloads the COSMIC cancer database of the latest COSMIC release into the current working directory.

References

If you use gget cosmic in a publication, please cite the following articles:

• Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836

• Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C, Dawson E, Fish P, Harsha B, Hathaway C, Jupe SC, Kok CY, Noble K, Ponting L, Ramshaw CC, Rye CE, Speedy HE, Stefancsik R, Thompson SL, Wang S, Ward S, Campbell PJ, Forbes SA. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 2019 Jan 8;47(D1):D941-D947. doi: 10.1093/nar/gky1015. PMID: 30371878; PMCID: PMC6323903.