[BioRuby] Final GSoC report

[Marjan Povolni]

http://blog.mpthecoder.com/post/29910330225/final-gsoc-report

*Summary*

Yesterday I tagged the 0.4 release of gff3-pltools, and that marks the end
of the summer. At least in GSoC terms. Should I say end of the project? I
don’t think so. The tools can still be improved, and the Ruby bindings
should follow.

The major changes since the last release include the following:

   - filtering functionality has been moved to a separate utility:
   gff3-filter, along with a new language for specifying filtering expressions,
   - conversion to table format of selected fields has been moved to a
   separate utility: gff3-select. However, the —select option is still part of
   gff3-filter,
   - gff3-ffetch is now fetching FASTA sequences from GFF3 and FASTA files
   for CDS and mRNA records and features,
   - man pages for utilities.

**
The original idea was to create a GFF3/GTF parser in D and Ruby bindings.
The Ruby bindings part didn’t work out because there is still no support
for D shared libraries in Linux, but instead there are now a few useful
command-line tools for processing GFF3 which can be used without
programming knowledge.

To me, the summer was fun, challenging, and a great experience. I even got
to meet my mentor in person, and other community members too, and to make
my first steps in bioinformatics. I even gave a small presentation at the
EU-codefest. What a summer it was!

Thanks to everybody who made it possible: Google, Open Bioinformatics
Foundation and my mentor Pjotr Prins.

--
Marjan