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

[Chris Fields]

I wouldn't mind helping out in maintaining blast.pm or RemoteBlast.pm, but
I'm still a bit 'green' with Perl and Bioperl objects and methods.  This
last fix was somewhat easy to spot (simple regex); the problems with saving
XML output (bug #1935) are a stumbling block here, though.  A new wrinkle
though, which limits the bug's severity: it does at least parse the XML
output as it will pull out accession numbers, which is a bit of a relief
(blastxml seems to be working).  It just won't save it, and using
$result->query_name still gives part of the RID, suggesting a regex messing
up somewhere, maybe in blastxml.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: Jason Stajich [mailto:jason.stajich at duke.edu]
> Sent: Tuesday, January 24, 2006 11:16 AM
> To: Chris Fields
> Cc: bioperl-ml List
> Subject: 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