templatePath = HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR;

SetDialogPrompt ("Select file containing paths:");
fscanf (PROMPT_FOR_FILE, "Lines", paths);


stdinRedirect = {};
stdinRedirect["00"] = "Universal";
stdinRedirect["01"] = "";	// replace within loop
stdinRedirect["02"] = "No/No";
stdinRedirect["03"] = "/tmp/temp.seq";


for (f = 0; f < Columns(paths); f = f + 1)
{
	// clean stop codons
	stdinRedirect["01"] = paths[f];
	ExecuteAFile (templatePath+"CleanStopCodons.bf", stdinRedirect);
	
	ExecuteCommands("DataSet ds = ReadDataFile(\"/tmp/temp.seq\");");
	DataSetFilter dsf = CreateFilter (ds,1);
	
	// clear out stop codons while we're at it
	
	DATA_FILE_PRINT_FORMAT = 4;
	
	dest = paths[f]^{{".seq"}{""}};
	
	ExecuteCommands("fprintf (\""+dest+".nex\", CLEAR_FILE, dsf);");
}