[Bioperl-l] parsing xml output

[Jason Stajich]

Whoops - sorry Warren - for some reason I had it in my mind that it  
was different.  So the blastxml parser should work fine.  The WUBLAST  
tab-delimited output is different than NCBI's -m8/9 though, right?

-jason


On May 18, 2006, at 7:57 PM, Warren Gish wrote:

> 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
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
> _______________________________________________
> 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