[Bioperl-l] Tandem Repeats finder parser

Eric Just e-just at northwestern.edu
Tue Mar 13 10:37:42 EDT 2007


Hi Stefan

Trf does indeed store the parameters in the filename, however it also
has a parameters line in the output file which is where I pull the
parameters from:

Parameters: 2 7 7 80 10 50 12

That may be a new feature, I'm using Tandem Repeats Rinder version
4.00   I was planning on using that since the file name is not
necessarily stable (a user can rename the file).  Sound reasonable?

Eric


On 3/13/07, Stefan Kirov <stefan.kirov at bms.com> wrote:
> Eric,
> The last time I used it, trf had a funny way of assigning filenames. Do
> you plan to parse the filenames and extract the parameters from there,
> or you are going to stick only to the content?
> If you can parse the filenames, that might be very useful.
> Stefan
>
> Chris Fields wrote:
> > I don't see a problem.  The best place for it is prob. in the
> > Bio::Tools namespace (unless you have other ideas).
> >
> > chris
> >
> > On Mar 12, 2007, at 5:02 PM, Eric Just 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
> >>
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>


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