[Biopython-dev] As of now (Thursday night, California)

[Michiel Jan Laurens de Hoon]

Iddo Friedberg wrote:
> test_Registry: I commented out the PDB and Swissprot sections.

I had a look at the PDB section in test_Registry. One problem seems to be the 
url. Now we are using

http://www.ebi.ac.uk/cgi-bin/emblfetch?db=PDB&format=default&style=raw&id=1BG3

but as Bill Barnard noticed a couple of weeks ago, this should be

http://www.ebi.ac.uk/cgi-bin/dbfetch?db=PDB&format=default&style=raw&id=1BG3

I fixed this in Bio/dbdefs/pdb.py.

The test_Registry still fails though. This seems to be due to the \n at the top 
of the EBI file at the second url. But this code seems to behave strangely 
anyway. Some sections in test_Registry (other than PDB and Swissprot) return a 
ParserPositionException in _parse_elements in Martel/Parser.py. How the test can 
pass anyway is a mystery to me.

Sorry, that's all I can say. Gotta run!

--Michiel.

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon