I'm looking for a programmatic way to access Ensembl or UCSC's genome browser using something like python or ruby. Perl is just not my thing, sadly. PyCogent seems to have something that I have not yet tested properly, but just wanted to ping the community before going ahead and coding something that might already exist.
Thanks Brad. I'm rather intrigued by the fact that biopython doesn't have anything for this. You know if anything is planned or discussed? Can't seem to find anything.
Ricardo; I'd prefer to see integration of these libraries with Biopython instead of reimplementing. We have PyCogent Ensembl targeted as part of our Google Summer of Code ideas:
I'd be interested in hearing how they work out for you since I haven't had a need to use them in my work yet.
Maybe I should apply for that project :) Sounds interesting.
Slightly off topic, but it surprises me how slow the Perl API is in comparison to other methods. I'm using Python and MySQLdb to directly query the MySQL database for some things and it's lightening fast in comparison to getting the same information using Perl. I can download information from 5 genomes in a fraction of the time it takes me to download 1 using Perl. Looking forward to see what PyCogent and PyGr can do for Ensembl using Biopython :)