[Biojava-dev] Fwd: [blast-announce] New Version of BLAST XML output

[Paolo Pavan]

I know Indeed. But actually my module is not just a parser, it is part of
an Input/output system for search results, I think biojava actually lacks
this. As seen in other Bio projects, aside with Sequence IO and Alignment
IO procedures it could have a Search result IO also.
The advantage is to define common data structures that models Hsp, Hits,
Results without taking care (ie. making abstraction) of the underlying
search program.

And all this work is already done.

Moreover you shoud admit that is more actractive to say that biojava has a
solution for parsing blast than to say that java has the possibility with
some efforts and prehaps some debugging to parse blast ;-)

I'm joking of course, sorry about that. But anyway I'm working on further
possible contributions that depends on this module.
Let me know.

Paolo

2015-05-05 21:29 GMT+02:00 Andreas Prlic <andreas at sdsc.edu>:

> Hi Paolo,
>
> Our policy has been for some time to recommend to create XML output with
> BLAST and parse all the required info from there. Due to the excellent
> support in Java to parse XML in many different ways we did not feel that
> there is a need for providing additional support on top of this in BioJava.
>
> For an example, you could create a data model from the XML schema using
> xjc and get an output file parsed into this datamodel using a JAXBContext.
>
> Andreas
>
>
>
> On Tue, May 5, 2015 at 7:21 AM, Paolo Pavan <paolo.pavan at gmail.com> wrote:
>
>> Thank you for the advice, Peter.
>> By the way, I have a blast parser system extending the biojava one that
>> was my intention to submit to the community if it is of any interest.
>> If it is so, I can rapidly check it against the new specification sent
>> and include it in the main project, If Andreas agree.
>>
>> Cheers,
>> Paolo
>>
>> 2015-05-05 15:42 GMT+02:00 Peter Cock <p.j.a.cock at googlemail.com>:
>>
>>> FYI - time to update all the Bio* parsers with the new BLAST XML
>>> variant...
>>>
>>> Peter
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: Mcginnis, Scott (NIH/NLM/NCBI) [E] <mcginnis at ncbi.nlm.nih.gov>
>>> Date: Tue, May 5, 2015 at 2:32 PM
>>> Subject: [blast-announce] New Version of BLAST XML output
>>> To: NLM/NCBI List blast-announce <blast-announce at ncbi.nlm.nih.gov>
>>>
>>>
>>> The NCBI is now making a new version of the BLAST XML available for
>>> testing.  Read about the changes and how to access BLAST results using
>>> the new XML at
>>> ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>>>
>>
>>
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>
>
>
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