[Pipet Devel] BlastXML

[J.W. Bizzaro]

I'm not anti-Java either (well...maybe I am :-).  You know, if any of these
non-Python tools are open source, they will be very useful for us to see how
it was done.  If we are interested in a pure Python core, we may be able to
translate some things to Python.

BTW, what translators are out there that translate ???-to-Python?

BlastXML should be good to look at because we want Blast searches to be
included in Loci.  Not that Loci will come with Blast, but we want it to be
one of the first things added to the core.  The same goes for FASTA.

> Many authors of *new and
> improved* programs, ie FASTA, have included parsible output into their
> programs.  This makes it easier to connect different analyses.

Something we must take a look at.  Have you looked into that Harry?

> IMHO a good
> thing.  Most MolbBio packages that I have seen are just a bag of unrelated
> pieces. meaning you can't run the output of BLAST or FASTA into CLUSTAL
> without a bit of work.

I couldn't have said it better myself! :-)  This is what Loci must _not_
become!  Whatever we use, it must pass this test:  Will it cause a break in
the Loci continuum?  Will Loci become "a bag of unrelated pieces"?  All Loci
data (in XML) should be able to be tossed around between the core parts of
Loci like a basketball at a Harlem Globetrotter's game!



Jeff
bizzaro at bc.edu



david.lapointe at umassmed.edu wrote:
> 
> Ok, I am one of those weasels too. I am not suggesting moving to Java but
> here's a piece that came down the BioWidget pipeline this week.
> 
> %%%%%%%%%%
> January 19, 1999
> 
> PharmTools SDK Suite(TM) (Early Access 1)
> 
> Announcing the availability of PharmTools SDK Suite(TM) (Early Access 1)
> from WorkingObjects.com for evaluation. PharmTools SDK is a collection
> of reusable Java frameworks and toolkits for use in the development of
> bioinformatics applications. This early access release includes: the
> Blast Parsing Framework and BlastXML-SDK. The Blast Parsing Framework is
> a set of design patterns and Java classes for processing native (i.e.,
> local) and NCBI website generated Blast2 reports. BlastXML-SDK extends
> the Blast Parsing Framework functionality to support the creation and
> processing of BlastXML documents.
> 
> The PharmTools SDK Suite may be downloaded from the WorkingObjects.com
> website at
> http://www.workingobjects.com.
> 
> %%%%%%%%%%%%
> 
> It's pretty large, about 100 kb of *.jar for the application, and 500 kb for
> the sdk.jar with a blastxml.dtd.  It has a functionality that relates to
> some discussion we had earlier this week on parsing the output of programs,
> which incidently is made easier by perl (regex).  Many authors of *new and
> improved* programs, ie FASTA, have included parsible output into their
> programs.  This makes it easier to connect different analyses. IMHO a good
> thing.  Most MolbBio packages that I have seen are just a bag of unrelated
> pieces. meaning you can't run the output of BLAST or FASTA into CLUSTAL
> without a bit of work.
> 
> David

-- 
J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/
--