Hi Steve,
> I would like to search for a specific repeat using fuzznuc. It is pretty easy
> using a regexp in preg (yes, I know preg should really only be used for
> protein sequences:-)) via
>
> preg -pattern '(TG{5,20}){2,10}'
>
> but is there a way to do something similar in fuzznuc, since I would like to
> introduce mismatches.
You could use dreg rather than preg :-)
Fuzznuc now accepts files with a pattern on each line:
% cat tg.pat
TG(5,20)TG(5,20)
TG(5,20)TG(5,20)TG(5,20)
TG(5,20)TG(5,20)TG(5,20)TG(5,20)
TG(5,20)TG(5,20)TG(5,20)TG(5,20)TG(5,20)
or, if you want to name them, ...
% cat tg.pat
>tg2
TG(5,20)TG(5,20)
>tg3
TG(5,20)TG(5,20)TG(5,20)
>tg4
TG(5,20)TG(5,20)TG(5,20)TG(5,20)
>tg5
TG(5,20)TG(5,20)TG(5,20)TG(5,20)TG(5,20)
You can use the file with:
% fuzznuc -pattern @tg.pat
Hope that helps,
Peter
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