TEMPLATE_INPUT.json

{
    
    "entrez": [{
    
        "request_limit" : 5,
        "sleep_time": 5,
        "email" : "EMAIL",
        "api_key" : "KEY"
        
    }],

    "blast" : [{

		"tax_include" : ["1236"],
		"tax_exclude" : [],
		"database" : "ref_prok_rep_genomes",
    	"e_val" : 10E-10,
    	"coverage_min": 0.5,
		"max_hits": 20000,
		"max_attempts": 3,
		"search_mult_factor": 2,
		"annotate": true,
		"extensive_search": true,
		"reverse_blast": true

    }],

    "hit_feature_detection" : [{

		"margin_limit": 5,
		"max_attempts": 10,
		"mult_factor" : 3

    }],

    "operon_assembly" : [{
		"feature_limit": 3,
		"intergenic_limit": 150,
		"use_ref_limit" : true,
		"ref_limit_margin" : 0.5    	

	}],
	
	"thread_limit": 10,

	"species_percent_id_limit": 0.45,

	"input_records" : ["WP_000373826.1", "WP_000173586.1", "WP_000821694.1", "WP_000562692.1", "WP_000778642.1"],

	"reference_genome_accession" : " NZ_CP025937.1",

	"reference_genome_assembly" : "NZ_00000000",

	"reference_genome_name": "Vibrio_cholerae_strain_A1552",

	"cache_dir": "./cache/",
	
	"color_code":[{

		"intergenic":"#000000",
		"WP_000373826.1":"#ffa200",
		"WP_000173586.1":"#68ff03",
		"WP_000821694.1":"#05eeff",
		"WP_000562692.1":"#4c05ff",
		"WP_000778642.1":"#ff05ea"

	}]
        
}