[Tutor] Sim4 output parser

Danny Yoo dyoo@hkn.eecs.berkeley.edu
Mon, 27 Aug 2001 17:27:57 -0700 (PDT)

On Mon, 27 Aug 2001, Tzu-Ming Chern wrote:

> Do you have any advice on how to start parsing sim4 output files?
> Specifically, I'd like to extract the start and end points of one of
> the matching pairs.

You might want to talk with the BioPython folks,


and see if they've written a sim4 parser already.  I've looked, but
haven't been able to find it myself yet.  If you can point us toward the
sim4 output specification, we might be able to cook something up that will
work for you.

There is a sim4 parser for BioPerl under the Bio::Tools::Sim4, so if
you're pressed for time, you can probably use BioPerl:


Good luck to you!