

Basic usage with a JSON input parameter file

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

  * output_format: tsv (default), json

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| * Show basic usage information                                                                                        |
| python3 src/tcell_mhci.py -h                                                                                          |
|_______________________________________________________________________________________________________________________|
| * List available methods and versions                                                                                 |
| python3 src/tcell_mhci.py -v                                                                                          |
|_______________________________________________________________________________________________________________________|
| * Run a binding prediction, specifying input parameters via a JSON file                                               |
| python3 src/tcell_mhci.py  -j [input_json_file]                                                                       |
| Example: python3 src/tcell_mhci.py  -j examples/binding.json                                                          |
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Basic usage with command-line parameters (limited support)
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| * Run a binding prediction with netmhcpan and print output to the screen                                              |
| python3 src/tcell_mhci.py --method=[method] --allele=[mhc] -p [peptide_or_protein_file]                               |
| Example: python3 src/tcell_mhci.py  -p examples/test.pep --method=netmhcpan --allele="HLA-A*02:01"                    |
|_______________________________________________________________________________________________________________________|
| * Run a binding prediction with netmhcpan and print output to a TSV file                                              |
| python3 src/tcell_mhci.py --method=[method] --allele=[mhc] -p [peptide_or_protein_file] -o [output_prefix]            |
| Example: python3 src/tcell_mhci.py  -p examples/test.pep --method=netmhcpan --allele="HLA-A*02:01" -o output          |
|_______________________________________________________________________________________________________________________|


IEDB internal usage and specialized use cases
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| * Split a large job into smaller units                                                                                |
| python3 src/tcell_mhci.py -j [input_json_file] --split --split-dir=[atomic_units_json_file_dir]                       |
| Example: python3 src/tcell_mhci.py -j examples/input_sequence_text.json --split --split-dir=parameter_units           |
|                                                                                                                       |
| 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.                               |
|_______________________________________________________________________________________________________________________|

*Usage caveats*

- Methods in the processing and immunogenicity group require using JSON inputs. See the 'examples' directory for
  sample configurations.  Future versions of this tool may add command-line parameter support.

- MHC-NP and MHCFlurry require the '-o' option to be specified.

