[Biopython] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour

[Michal]

Hi Peter,
Do you have the script which read

https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml


and what would be the correct output?

Thank you in advance.

Cheers,
Michal

On 05/03/2011 11:31 PM, Chris Fields wrote:
> Haven't tried this using the latest BLAST+ myself, but it doesn't surprise me too much.  Also agree re: some kind of bug tracking with NCBI; I believe they have an internal one, but it would be nice to have a public interface to it.
>
> chris
>
> On May 3, 2011, at 4:24 AM, Peter Cock wrote:
>
>> Hello all,
>>
>> I've CC'd the BioPerl, BioRuby, BioJava and Biopython development mailing
>> lists to make sure you're aware of this, but can we continue any discussion
>> on the cross-project open-bio-l mailing list please?
>>
>> I noticed that recent versions of BLAST are not using a single<iteration>
>> block for each query, which was the historical behaviour and assumed
>> by the Biopython BLAST XML parser. This may be a bug in BLAST.
>> See link below for an example.
>>
>> Has anyone else noticed this, and has it been reported to the NCBI yet?
>>
>> Thanks,
>>
>> Peter
>>
>> (Not for the first time, I wish there was a public bug tracker for BLAST,
>> or at least a private bug tracker so we could talk about issues with an
>> NCBI assigned reference number.)
>>
>> ---------- Forwarded message ----------
>> From: Peter Cock<p.j.a.cock at googlemail.com>
>> Date: Wed, Apr 20, 2011 at 6:08 PM
>> Subject: Interesting BLAST 2.2.25+ XML behaviour
>> To: Biopython-Dev Mailing List<biopython-dev at biopython.org>
>>
>>
>> Hi all,
>>
>> Have a look at this XML file from a FASTA vs FASTA search
>> using blastp from  BLAST 2.2.25+ (current release), which
>> is a test file I created for the BLAST+ wrappers in Galaxy:
>>
>> https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml
>>
>> I just put it though the Biopython BLAST XML parser, and
>> was surprised not to get four records back (since as you
>> might guess from the filename, there were four queries).
>>
>> It appears this version of BLAST+ is incrementing the
>> iteration counter for each match... or something like that.
>>
>> Has anyone else noticed this? I wonder if it is accidental...
>>
>> Peter
>>
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>
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