[Bioperl-l] parsing xml output

[Christopher Fields]

Just to make sure everybody knows, if you use bioperl v1.5.1, 
SearchIO::blastxml uses XML::Parser which should come with most recent perl 
distributions.   The bioperl-live version has switched over to XML::SAX for SAX2 
parsing and it is recommended that you install XML::SAX::ExpatXS as well for 
faster parsing. 

Chris

---- Original message ----
>Date: Thu, 18 May 2006 18:57:03 -0500
>From: "Warren Gish" <gish at watson.wustl.edu>  
>Subject: Re: [Bioperl-l] parsing xml output  
>To: "'Hubert Prielinger'" <hubert.prielinger at gmx.at>
>Cc: bioperl-l at bioperl.org
>
>Just to clarify, the XML output from WU-BLAST conforms to the standard
>NCBI_BlastOutput.dtd.  Technically, contents of data fields could still be
>incompatible, but care was taken to ensure compatibility.  If someone
>identifies a difference that prevents parsing or proper interpretation of
>the WU-BLAST output, please let me know.
>Regards,
>--Warren 
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org 
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
>> Jason Stajich
>> Sent: Thursday, May 18, 2006 5:23 PM
>> To: Hubert Prielinger
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] parsing xml output
>> 
>> we don't parse WU-BLAST XML at this time.  We'd welcome someone  
>> contributing this.
>> 
>> ncbi XML is parsed with blastxml format.
>> 
>> -jason
>> On May 18, 2006, at 4:41 PM, Hubert Prielinger wrote:
>> 
>> > hi,
>> > what is the best way to parse NCBI- and WU- Blast XML output....
>> > and is it possible to parse both with the same parser, or 
>> differ their
>> > XML output...
>> >
>> > thanks
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> --
>> Jason Stajich
>> Duke University
>> http://www.duke.edu/~jes12
>> 
>> 
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>
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