[BioRuby] Google Summer of Code project ideas

[Mic]

HI Raoul,
Analogous to Samfile, a Tabixfile allows fast random access to compressed
and tabix indexed tab-separated file formats with genomic data:

*import pysam*
*tabixfile = pysam.Tabixfile( "example.gtf.gz" )*
*
*
*for gtf in tabixfile.fetch('chr1', 1000, 2000):*
*    print gtf.contig, gtf.start, gtf.end, gtf.gene_id*
*
*
*
*
I am not suitable for a mentor, because I have not used Ruby for years. I
just observe BioRuby and try give some ideas.

Cheers,

On Tue, Mar 6, 2012 at 6:09 PM, Raoul Bonnal <bonnal at ingm.org> wrote:

>  Hi Mic,
>
> >* a ruby version of
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232365/?tool=pubmed
> If you want to help us with GSoC please add it to the list and put
> yourself as a mentor ( later you’ll need to register yourself as a mentor),
> for us (the panel) any bioruby developer/user can be a mentor, it’s not
> much work and you’ll not be alone :)
>
>
> >a ruby interface for tabix ( http://samtools.sourceforge.net/tabix.shtml) see pysam
> http://code.google.com/p/pysam/source/browse/tests/tabix_test.py?r=2fff972c6b60390e4962d3f46f7c269acd9aa33e
>  Is it an interface to sam/bam ? Have you see this
> https://github.com/helios/bioruby-samtools project ? Can you evaluate the
> main differences between the two projects ?
>
> Please add them to GSoC (on our wik) in any case, we’ll keep there the
> list of desired things. If you do not have time to be a mentor just write
> the projects and maybe someone will lead it.
>
> Thanks a lot!
>
>
> On 06/03/12 02.18, "Mic" <mictadlo at gmail.com> wrote:
>
>
>    - a ruby version of
>    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232365/?tool=pubmed
>
>
>
>
> * a ruby interface for tabix ( http://samtools.sourceforge.net/tabix.shtml) see pysam
> http://code.google.com/p/pysam/source/browse/tests/tabix_test.py?r=2fff972c6b60390e4962d3f46f7c269acd9aa33e
>
>
> On Sat, Mar 3, 2012 at 9:15 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
>
> Thanks !
>
> Rob is aware that our page is ready to go.
>
> Good job BioRubyGuys
>
>
> On 02/03/12 15.04, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:
>
> > On 10 Feb, Robert Buels wrote (posted by Chris Field):
> >> Hi all,
> >>
> >> I'm going to be OBF project admin again this year for Google Summer of
> >> code.  OBF's application is due in a couple of weeks, and we need to
> update
> >> our project ideas on the OBF wiki page and on each project's individual
> wiki
> >> pages.
> >>
> >> So, for each of the OBF projects that wants to do GSoC again this year,
> >> please:
> >>
> >> a.) Update the list of project ideas on your project's GSoC page
> >> (BioPython, BioPerl, BioRuby, etc).  Add new ones, remove ones that have
> >> already been done or no longer relevant, etc.
> >>
> >> b.) Update the list of project ideas on the main OBF GSoC page
> >> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.
> >>
> >> c.) Let me know via email that you have done so and it's ready for
> Google
> >> to peruse.
> >>
> >> Please have the updates done, if possible, by this Friday (March 11).
> The
> >> number and quality of the project ideas are part of the evaluation
> process
> >> for whether OBF is accepted as a Summer of Code organization again this
> >> year, so let's come up with some good ones.  :-)
> >>
> >> Rob
> >>
> >> ----
> >> Robert Buels
> >
> > Hi BioRuby folk,
> >
> > You seem to have been the most organized Bio* project for GSoC so far,
> and
> > have
> > put together good set of GSoC project ideas by Rob's target date. Well
> done :)
> >
> > Is the list here complete now?
> > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code
> >
> >     3.1.1 Write the world's fastest parallelized GFF3/GTF parser in D,
> > for Ruby FFI
> >     3.1.2 Extend bio-alignment plug-in with Multiple Alignment Format
> > -MAF- parser (FFI?)
> >     3.1.3 Testing framework for biogem plugins
> >     3.1.4 Adding social networking functionality to BioRuby.org
> >     3.1.5 Update bio-images a plugin to represent bio-object with cool
> images
> >     3.1.6 Update to the Ruby Ensembl API
> >
> > I noticed "Testing framework for biogem plugins" was missing on the OBF
> > summary page, so I added it:
> > http://www.open-bio.org/wiki/Google_Summer_of_Code
> >
> > Regards,
> >
> > Peter
> >
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>
>
>
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