[Biojava-dev] BioJava3 release - code organization for "old" code - Blast info

Tue Jan 11 18:27:15 UTC 2011

Hi Keith,

 I'm interested in helping you with the Blast parsing too, code wise. :)

Cheers,
Marco.

On Tue, Jan 11, 2011 at 2:36 PM, Keith Perry <KPerry at idtdna.com> wrote:

> Thanks for the info Scooter!  I will take a look at the effort of creating
> a nice Blast xml parser (similar to yours in BlastXMLQuery) that includes
> creating a blast record (like the biopython version
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc88).  I
> checked out the biojava3-ws module briefly, but from what I can tell it
> doesn't have a "blast record" class either.  I am not sure if the
> biojava3-ws module also includes automated throttling (so NCBI doesn't block
> you), but that would be a nice feature as well.  I might start out using the
> biojava3-ws, but we might be going the local route (with the blastx
> executables), so I would like to build a wrapper for that as well.
>
> Anyway, anything that might be helpful to others, I will be sure to submit
> back, and I will keep the modularity going on.  That's how I usually try to
> write my code, although it doesn't always start like that ;)
>
> -----Original Message-----
> From: Scooter Willis [mailto:HWillis at scripps.edu]
> Sent: Tuesday, January 11, 2011 9:54 AM
> To: Keith Perry
> Subject: Re: [Biojava-dev] BioJava3 release - code organization for "old"
> code - Blast info
>
> Keith
>
> For interfacing with Blast I have taken the route of loading the results as
> XML and using XPATH to query what I need. A simple example
> BlastXMLQuery.java in the biojava3-genome module. If you have specific
> requirements for interfacing with Blast would welcome any code you can
> contribute by either migrating the 1.7 module or starting fresh and focusing
> on parsing the XML into useable classes.
>
> There is a biojava3-ws module that will Query NCBI Blast via web services.
> Not sure if that is close to what you need. I haven't used it.
>
> The task of rewriting and porting all the features of BioJava 1.7 would be
> a huge undertaking for an all volunteer organization. Our primary focus was
> modularizing the code and minimize the interdependencies as much as
> possible. The biojava3-core module provides the glue across multiple modules
> for those that need to incorporate multiple modules in their application.
> With the modularization it makes it easier to have developer work on very
> specific functionality allowing biojava3 to be a little more dynamic.
>
> Will let Andreas comment on packaging everything up as one zip file. You
> probably won't need everything which allows you to download the individually
> the modules you need. If you are able to work on a blast interface it would
> be great if you could return sequence objects in Biojav3 core. If you find
> you are missing anything in the api I can work on getting it added in.
>
> Thanks
>
> Scooter
>
>
> On Jan 11, 2011, at 10:30 AM, Keith Perry wrote:
>
> > Hi all,
> > A couple of notes on the BioJava3 release.  I am not sure I would assume
> that everyone is using Maven (we are using Gradle at our company).  Could
> someone please package up the "manual download" files into a single
> zip/jar/tar.gz or some type of archive format (I would greatly appreciate
> it)?  Downloading 18 files individually is a pain.
> >
> > I was pretty excited to see BioJava3 to get released, but then I realized
> that no support at all for blast (as far as I can tell).  It looks like you
> need to use the old biojava-legacy stuff in biojava 1.7.  Is there something
> that I could do to get this example:
> http://www.biojava.org/wiki/BioJava:CookBook:Blast:Parser up to the new
> BioJava3 level?  If I need to take a couple modules and refactor, I would be
> willing to do it (or at least give it a try).
> >
> > On another note, is there some type of chart that shows feature/version
> for all the features in both 1.7 and biojava3.  It would be nice for those
> new to the project, and it might let other developers know what holes
> biojava3 still has (as compared to the legacy).
> >
> > Thanks,
> >
> > Keith B. Perry | 319.626.9677 | kperry at idtdna.com | Integrated DNA
> Technologies > Bioinformatics Team > Software Systems Engineer
> >
> >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>