We can refer *.js file from SharePoint visual part (*.ascx) file via <SharePoint:ScriptLink> tag. Example
<SharePoint:ScriptLink ID="ScriptLink1" runat="server" Language="javascript" Name="/_layouts/15/css/clienttemplates.js" />
OR
<script src="/_layouts/15/autofill.js" type="text/javascript"> </script>
