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