/*
SetDialogPrompt ("Select file containing paths:");

fscanf (PROMPT_FOR_FILE, "Lines", paths);
*/

fscanf ("/home/art/wip/swenson/dutch_v3/hyphy/_paths.txt", "Lines", paths);

/* path_to_trees = "/Users/apoon/wip/swenson/dutch_v2/reconstruct"; */
_path_to_trees = "/home/art/wip/swenson/dutch_v3/hyphy";

for (_path = 0; _path < Columns(paths); _path = _path+1)
{
	/*
		it is VERY important to use NEXUS files because these have been
		screened for stop codons!!!
	*/
	indices = paths[_path]$"/[A-Za-z0-9_]+\.nex";
	prefix = (paths[_path])[indices[0]][indices[1]];
	treefile = prefix^{{"\.nex"}{".nwk"}};
	outfile = prefix^{{"\.nex"}{".out"}};
	
	stdinRedirect = {};
	
	stdinRedirect["00"] = "Universal";	/* Genetic code */
	stdinRedirect["01"] = paths[_path];
	stdinRedirect["02"] = "Global"; /* Model options */
	stdinRedirect["03"] = "012345";	/* GTR */
	stdinRedirect["04"] = _path_to_trees+treefile; /* file containing trees */
	stdinRedirect["05"] = "100";	/* number of samples */
	stdinRedirect["06"] = _path_to_trees+outfile;
	
	fprintf (stdout, stdinRedirect, "\n");

	ExecuteAFile ("mpi_codon_model.bf", stdinRedirect);
}