benchmarking_parameters.json

{
        "datasets": {
                "mhc_ligands": {
                        "lengths": [9],
                        "mismatches": 0,
                        "query": "queries/mhc-ligands-test.fasta",
                        "proteome": "proteomes/human.fasta",
                        "expected": "expected/mhc-ligands-expected.tsv"
                },
                "milk": {
                        "lengths": [15],
                        "mismatches": -1,
                        "query": "queries/milk-peptides-test.fasta",
                        "proteome": "proteomes/human.fasta",
                        "expected": "expected/milk-peptides-expected.tsv"
                },
                "coronavirus": {
                        "lengths": [8, 9, 10, 11, 12, 13, 14, 15],
                        "mismatches": 2,
                        "query": "queries/coronavirus-test.fasta",
                        "proteome": "proteomes/betacoronaviruses.fasta",
                        "expected": "expected/coronavirus-expected.tsv"
                },
                "neoepitopes": {
                        "lengths": [15],
                        "mismatches": 3,
                        "query": "queries/neoepitopes-test.fasta",
                        "proteome": "proteomes/human.fasta",
                        "expected": "expected/neoepitopes-expected.tsv"
                }
        },
       
        "methods": [
                {
                        "name": "PEPMatch",
                        "text_shifting": 0,
                        "method_parameters":{
                                "output_format": "dataframe"
                        }
                },
                {
                        "name": "NmerMatch",
                        "text_shifting": 0,
                        "method_parameters":{
                                "nmer_script_path": "NmerMatch/bin/run_nmer_match.pl",
                                "perl_exe": "",
                                "perl_include_path": "",
                                "catalog_master_dir": "",
                                "output_master_dir": ""
                        }
                },
                {
                        "name": "blast",
                        "text_shifting": 0,
                        "method_parameters":{
                                "bin_directory": "../bin"
                        }
                },
                {
                        "name": "diamond",
                        "text_shifting": 0,
                        "method_parameters":{
                                "bin_directory": "../bin"
                        }
                },
                {
                        "name": "mmseqs2",
                        "text_shifting": 0,
                        "method_parameters":{
                                "bin_directory": "../bin/"
                        }
                },
                {
                        "name": "horspool",
                        "text_shifting": 1,
                        "method_parameters":{}
                },
                {
                        "name": "boyer_moore",
                        "text_shifting": 1,
                        "method_parameters":{}
                },
                {
                        "name": "knuth_morris_pratt",
                        "text_shifting": 1,
                        "method_parameters":{}
                },
                {
                        "name": "z",
                        "text_shifting": 1,
                        "method_parameters":{}
                }
        ]
}