[Bioperl-l] RemoteBlast.pm and Bio::SearchIO::blast.pm -partially resolved

[Chris Fields]

Jason, 

I have worked out all the problems with RemoteBlast.pm and posted a patched
version to Bugzilla (http://bugzilla.bioperl.org/show_bug.cgi?id=1935).  The
main problem was that RemoteBlast::save_output was not looking for XML
output when dumping from the tempfile to the saved file (it only looked for
the text header).  That is fixed.  The other problems mentioned were due to
differences in mapping key=>value pairs between blast and blastxml and a
problem in my own script.  It passed all tests using 'perl t/RemoteBlast.t'
with debugging set.

See if anybody else out there can test them out.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
> bounces at portal.open-bio.org] On Behalf Of Jason Stajich
> Sent: Tuesday, January 24, 2006 11:16 AM
> To: Chris Fields
> Cc: bioperl-ml List
> Subject: [Bioperl-l] Re: RemoteBlast.pm and Bio::SearchIO::blast.pm -
> partially resolved
> 
> Thanks Chris - I don't know when I'll have time to check in bugs so
> anyone else who has commit access feel free to give these a whirl and
> check in.
> 
> I would propose making the XML default but allowing the text version
> to still be supported in the event that someone has setup their own
> local NCBI BLAST Web interface which still supports the simple Text
> output.
> 
> -j
> 
> On Jan 24, 2006, at 12:09 PM, Chris Fields wrote:
> 
> > I submitted two bugs on Bugzilla to describe recent problems with
> > RemoteBlast.pm and SearchIO::blast.pm
> >
> > http://bugzilla.bioperl.org/show_bug.cgi?id=1934
> > http://bugzilla.bioperl.org/show_bug.cgi?id=1935
> >
> > Today I submitted a patched version of Bio::SearchIO::blast.pm
> > which should
> > fix the text parsing issue for old (2.2.12) and new (2.2.13)
> > versions of
> > NCBI's BLAST; the bug link above describes the problem and the
> > fix.  Problem
> > is, I know it will likely break again b/c NCBI will probably change
> > text
> > output in a future BLAST version.  I also agree with Jason about
> > changing
> > the default for SearchIO to XML.  So, does text output parsing through
> > blast.pm need to be deprecated in favor of XML, or should both be
> > available?
> >
> > Christopher Fields
> > Postdoctoral Researcher - Switzer Lab
> > Dept. of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> 
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
> 
> 
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