Command line

Genemaps main functions (map_ids, map_dataframe and fetch_mapping) are also accessible via the command line. Each of these functions is implemented in its own subcommand. Examples are shown below.

Mapping ids

A list of gene ids can be mapped from the command line as follows:

genemap map_ids ensembl \
    --from_type symbol --to_type ensembl \
    --host http://aug2014.archive.ensembl.org \
    TP53 BRCA1 PPP1R12A

This commands prints the translated identifiers to the console.

Mapping dataframes

DataFrames (in tab-separated format) can be mapped using the following command:

genemap map_datataframe ensembl \
    --from_type symbol --to_type ensembl \
    --host http://aug2014.archive.ensembl.org \
    input.txt mapped.txt

In this example, the translated DataFrame is written to mapped.txt.

Fetching maps

Mappings can also be extracted using the fetch_mapping subcommand:

genemap fetch_mapping ensembl \
    --from_type symbol --to_type ensembl \
    --host http://aug2014.archive.ensembl.org \
    mapping.txt

This writes the mapping (a DataFrame containing two columns with the source/target identifiers) to the mapping.txt output file.