[GSoC] Final GSoC report
Marjan Povolni
marian.povolny at gmail.com
Tue Aug 21 19:11:01 UTC 2012
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
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