

Basic usage

  python3 src/match.py -j <input_json_file> --proteomes-path <proteomes_path> \
  [-o] <output_prefix> [-f] <output_format>

  * output_format: tsv (default), json
 _______________________________________________________________________________________________________________________
| * List all available commands.                                                                                        |
| python3 src/match.py -h                                                                                               |
|_______________________________________________________________________________________________________________________|
| * Make prediction with all input parameters in JSON file                                                              |
| python3 src/match.py -j [input_json_file]                                                                             |
| Example: python3 src/match.py  -j examples/pepmatch.json --proteomes-path=./proteomes-20240313                        |
|_______________________________________________________________________________________________________________________|
| * Make prediction with all input parameters in JSON file and write result to a JSON file                              |
| python3 src/match.py  -j [input_json_file]  -o [output_prefix] -f json                                                |
| Example: python3 src/match.py  -j examples/pepmatch.json -o output -f json --proteomes-path=./proteomes-20240313      |
|_______________________________________________________________________________________________________________________|

- The PEPMATCH_PROTEOMES_PATH environment can be specified in place of the --proteomes-path command-line switch

