

Basic usage with a JSON parameter file (limited support)

  python3 src/run_pepx.py -j <input_json_file> [-o] <output_prefix> [-f] <output_format>

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| * List all available commands.                                                                                        |
| python3 src/run_pepx.py -h                                                                                            |
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| * Make prediction with all input parameters in JSON file                                                              |
| python3 src/run_pepx.py -j [input_json_file] -p <path_do_db>                                                          |
| Example: python3 src/run_pepx.py -j examples/example.json -p pepx.sqlite                                              |
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| * Make prediction with all input parameters in JSON file and write result to a JSON file                              |
| python3 src/run_pepx.py -j [input_json_file] -o [output_prefix] -f json -p <path_to_db>                               |
| Example: python3 src/run_pepx.py -j examples/example.json -o output -f json -p pepx.sqlite                            |
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Basic usage with command-line parameters

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| * Check peptides for expression at the gene level                                                                     |
| python3 src/run_pepx.py -q gene -s <datasource> -d <dataset_id> -p <path_do_db> <peptides>                            |
| Example: python3 src/run_pepx.py -q gene -s CCLE -d 329 -p pepx.sqlite  FVQMMTAK MRYVASYL EDIISFIK                    |
|                                                                                                                       |
| * Submit input sequences as TSV                                                                                       |
| Example: python3 src/run_pepx.py -i examples/example.tsv -q gene -s CCLE -d 329 -p <PATH_TO_DB>                       |
|                                                                                                                       |
| * Output tabular result to terminal                                                                                   |
| Example: python3 src/run_pepx.py -q gene -s CCLE -d 329 -f tsv -p <PATH_TO_DB> FVQMMTAK MRYVASYL EDIISFIK             |
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| * Output result in JSON format to terminal                                                                            |
| Example: python3 src/run_pepx.py -q gene -s CCLE -d 329 -f json -p <PATH_TO_DB> FVQMMTAK MRYVASYL EDIISFIK            |
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| * Save the result into a TSV file                                                                                     |
| Example: python src/run_pepx.py -q gene -s CCLE -d 329 -o pepx_result -f tsv -p <PATH_TO_DB> FVQMMTAK MRYVASYL        |
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