[Biopython] problem with KEGG.REST.kegg_conv

[Felix Heeger]

Hi,

first of all thanks for the awesome library. 

Here is my problem: I am trying to to use the KEGG.REST.kegg_conv
function to translate NCBI GIs to kegg gene names.

For example I think this should work:

> kegg_conv("genes","ncbi-gi:16130957")

But I get an error from Biopython:

> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/local/lib/python2.7/dist-packages/Bio/KEGG/REST.py", line 252, in kegg_conv
>     raise Exception("Bad argument target_db or source_db for kegg conv request.")
> Exception: Bad argument target_db or source_db for kegg conv request.

Looking at the code, I think the only accepted input for the function
would look something like this:

> kegg_conv("genes","ncbi-gi")

This does indeed not cause a error from Biopython, but is clearly
missing the information *which* GI I want to convert and also gives my
a HTTP Error because Kegg does not accept the resulting URL
(http://rest.kegg.jp/conv/genes/ncbi-gi).

Is this a problem with the kegg_conv function or am I missing something?

Cheers,
felix