[Bioperl-l] Tandem Repeats finder parser

Eric Just e-just at northwestern.edu
Wed Mar 14 11:00:21 EDT 2007


Bio::Tools::TandemRepeatsFinder is now in CVS.  It only parses the
data file that is created when TRF is run with the -d option.  It does
not parse any of the html files that are produced.  Look at the POD
for a quick usage summary as well as t/TandemRepeatsFinder.t for how
to extract each piece of data.

Let me know if you have any questions or suggestions.

(From TRF docs:)
-d: A data file is produced if this option is present. This file is a
text file which contains the same information, in the same order, as
the summary table file, plus consensus pattern and repeat sequences.
This file contains no labeling and is suitable for additional
processing, for example with a perl script, outside of the program.


On 3/13/07, Mark Johnson <johnsonm at gmail.com> wrote:
> I'm going to need a trf parser.  I'd be happy to use yours instead of
> writing one myself.  I'll be eagerly watching cvs.  8)
> On 3/12/07, Eric Just <e-just at northwestern.edu> wrote:
> > Hi there,
> >
> > I have written a simple parser for Tandem Repeats Finder output.   Is
> > there any interest in including this module in Bioperl?  If so, I will
> > conform it to Bioperl standards, write some tests, then send it to
> > whomever is interested.
> >
> > Eric
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >

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