pjotr.public14 at thebird.nl
Wed Jul 7 16:17:40 UTC 2010
On Wed, Jul 07, 2010 at 10:56:46AM -0400, Naohisa Goto wrote:
> As far as I know, no Ruby/BioRuby components like BioPerl's
> Bio::Assembly are available.
> Currently, sequences and qualities formatted in Fasta, FASTQ, ABI, SCF
> and other file formats can be treated with BioRuby.
> However, I don't know good ways to handle assembly output data.
Before rewriting from scratch, see if there are useful C/C++ libraries
we can map to with SWIG (BioLib project). I can help with that.
Alternatively check what is written in JAVA - JRuby makes accessing
anything on the JVM rather trivial, these days. Or even interface to
Perl libraries and map those to Ruby.
I would start with that, then see what is a useful feature set for
BioRuby. Design it in such a way that external libraries can be
replaced in time, when someone feels like writing the support.
We are getting BioRuby plugin support, allowing for flexible
approaches to adding functionality.
More information about the BioRuby