retrieve_relevant_genomes_config.json

{
	"analysis_name" : "name_of_the_run",
	
	"proteins_filename" : "delta_phage_proteins.txt",
	
	"blast_parameters" : {
    	
    	"database" : "nr",
    	"taxid" : 10239,
    	"eval_threshold" : 1E-10,
    	"qcov_threshold" : 0.75,
    	"minimum_genome_length" : 10000,
    	"attempts_limit" : 5
    	
	},
	
	"entrez_parameters" : {
    	   	
    	"email" : "your@email.address",
    	"api_key" : null,
    	"sleep_time" : 1
	
	},
	
	"alpha_phages_file_name" : "alphaproteobacteria_phages_list.json",

	"plitropic_phages_file_name" : "pilitropic_phages_list.json",
	
	"flagellotropic_phages_file_name" : "flagellotropic_phages_list.json",
	
	"use_tblastn_hits_from_previous_run" : false
	
}