can't apply styles to string from external source


I've been reading up a bit on this but couldnt find a solution, so maybe
someone here has some good advice.

I am running some data through BioRuby (which, among other things, calls
an external program from the shell). This procedure returns a BioRuby
object, similar to an array or hash. In my rails application, each
element of this object can be puts'd and then, for example, gsub'ed, but
the puts'd object will not accept any font-modifications, like
font-size, font-style or whatever else via <span class='some-style'><%=
bioruby_object.string %></span>.
What could be the reason for this behavior?