[BioRuby] Bio::Assembly

Pjotr Prins pjotr.public14 at thebird.nl
Wed Jul 7 16:17:40 UTC 2010

Hi Chase,

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.


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