Command Line Interface

PEMT commands.

pemt

Run PEMT.

pemt [OPTIONS] COMMAND [ARGS]...

run-chemical-extractor

Extract chemicals for genes of interest

pemt run-chemical-extractor [OPTIONS]

Options

--name <name>

Required Name of the analysis that is to be run

--data <data>

Required Path to tab-separated gene data file

--input-type <input_type>

Type of data file i.e. ‘tab’ for tsv or ‘comma’ for csv files

--uniprot, --no-uniprot

Boolean value indicating whether the gene data file has uniprot ids or not.

run-patent-extractor

Extract patent for filtered chemicals

pemt run-patent-extractor [OPTIONS]

Options

--name <name>

Required Name of the analysis that is to be run

--os <os>

The OS system on which is the script is running

Options:

linux | mac | windows

--chromedriver-path <chromedriver_path>

Required The path where the chromedriver can be found on the users computer

--year <year>

The year from which you want to retrive patents from

--chemical, --no-chemical

Boolean value indicating whether the chemical data is provided by the user or not

--chemical-data <chemical_data>

Path to tab-separated chemical data file with single column of chembl_ids

run-pemt

Run the PEMT tool with gene data

pemt run-pemt [OPTIONS]

Options

--name <name>

Required Name of the analysis that is to be run

--data <data>

Required Path to tab-separated gene data file

--input-type <input_type>

Type of data file i.e. ‘tab’ for tsv or ‘comma’ for csv files

--uniprot, --no-uniprot

Boolean value indicating whether the gene data file has uniprot ids or not.

--chromedriver-path <chromedriver_path>

Required The path where the chromedriver can be found on the users computer

--os <os>

The OS system on which is the script is running

Options:

linux | mac | windows

--year <year>

The year from which you want to retrive patents from