[BioSQL-l] Relationship between Gene CDS and mRNA Seqfeatures

[Peter]

On Thu, Nov 4, 2010 at 12:34 PM, Nicholas Thrower <throwern at msu.edu> wrote:
>
> Peter,
>
> Thank you for the quick answer.
>
> Yes, I used the BioPerl wrapper to load the data.
>
> I was interested in using BioRuby but was not able to find ruby scripts
> comparable to load_ncbi_taxonomy.pl and load_seqdatabase.pl.
>
> -Nick

Hi Nick,

Note that while the load_ncbi_taxonomy.pl script is written in perl it is
part of BioSQL, not BioPerl. To me there doesn't seem to be much
benefit in rewriting it in Ruby (or Python).

I don't know about BioRuby, but the BioPerl script load_seqdatabase.pl
doesn't have a direct equivalent in Biopython. Including a selection of
scripts with Biopython is something we've considered but haven't really
tackled yet. However, it is just a few of lines to do an import in BioSQL
using our SeqIO parsing framework. See this wiki page for more details:
http://www.biopython.org/wiki/BioSQL

You may get more help on the BioRuby mailing list...

Regards,

Peter