IEDB Peptide Variant Comparison - 0.2 Beta

This tool mostly serves as a wrapper around the TC1 tool to support running paired peptide lists and collating the
outputs.  Follow the 'IEDB internal usage' section below.  Future releases will aim to be more user-friendly for
non-IEDB usage.

Basic usage
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| * Print this help message                                                                                             |
| python3 src/run_pvc.py -h                                                                                             |
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| * Run a Peptide Comparison prediction, specifying input parameters via a JSON file                                    |
| python3 src/run_pvc.py  -j [input_json_file]  [-o] <output_prefix> [-f] <output_format>                               |
| Example: python3 src/run_pvc.py  -j examples/input_sequence_text.json -o output -f json                               |
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IEDB internal usage
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| * Preprocess inputs and define jobs (commands) to run                                                                 |
| python3 src/run_pvc.py -j [input_json_file] --split --split-dir=[split_inputs_dir]                                    |
| Example: python3 src/run_pvc.py -j examples/input_sequence_text.json --split --split-dir=job_example/split_inputs                 |
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| Among other outputs, a 'job_descriptions.json' file will be created that will specify the commands to use for each    |
| individual job.  A future release of NG Tools may include code for managing these jobs.                               |
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| Sepearate jobs, calling the tcell_mhci.py script, will be created for peptide A and peptide B. A final aggregation    |
| job, that merges these outputs together, is also created and will look similar to:                                    |
|                                                                                                                       |
| python3 src/run_pvc.py --aggregate \                                                                                  |
| --peptideA-result-path=[path_to_peptideA_results] \                                                                   |
| --peptideB-result_path=[path_to_peptideB_results] \                                                                   |
| --aggregate-output-path=[path_to_final_results]                                                                       |
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