[Bioperl-l] correction to docs for Bio::SearchIO::axt

Cathy Riemer cathy at bio.cse.psu.edu
Sat Sep 16 12:43:14 EDT 2006


Chris and Jason,

Thanks for taking care of this.  One small suggestion: to add the
word "many" before "precomputed", since some sites might provide
LAV (or other formats).

-Cathy


On Sat, Sep 16, 2006 at 08:55:27AM -0500, Chris Fields wrote:
> Jason, Cathy,
> 
> I changed the POD description to the following in CVS:
> 
> ....
> 
> =head1 DESCRIPTION
> 
> This is a parser and event-generator for AXT format reports.  BLASTZ
> reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally
> in LAV format but are commonly post-processed to AXT format; precomputed
> BLASTZ reports, such as those found in the UCSC Genome
> Browser, are in AXT format.   This parser will also parse any
> AXT format produced from any lav report and directly out of BLAT.
> ...
> 
> 
> Chris
> 
> On Sep 16, 2006, at 12:21 AM, Jason Stajich wrote:
> 
> >right - I guess I meant the only way to get BLASTZ into our system is
> >lav -> axt.
> >
> >I will see if someone wants to update the module synopsis to clarify
> >this point for users or I will get to it when I have time.
> >
> >On Sep 15, 2006, at 11:18 PM, Cathy Riemer wrote:
> >
> >>Hello Jason,
> >>
> >>I noticed an error in the documentation page for the
> >>Bio::SearchIO::axt parser at
> >><http://search.cpan.org/~birney/bioperl/Bio/SearchIO/axt.pm>.
> >>
> >>The page states that "AXT format reports [are] typically produced
> >>by BLASTZ", but actually BLASTZ produces lav output, not axt.
> >>Sites that provide pre-computed BLASTZ alignments in axt format
> >>(such as UCSC's Genome Browser) convert them from lav to axt in
> >>a post-processing step.
> >>
> >>-Cathy
> >>
> >>---
> >>Cathy Riemer
> >>Center for Comparative Genomics and Bioinformatics
> >>Penn State University
> >
> >_______________________________________________
> >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
> 
> 
> 


More information about the Bioperl-l mailing list