[Biopython] Error in Querying the KEGG API

[Peter Cock]

Dear Iuwen,

Thank you for emailing us. This example looks wrong, or at least
out of sync with the actual code. The handle style is also quite
old (not explicitly closing the file handles).

I've not worked out what happened, but Biopython 1.65 added
Bio.KEGG.REST as a new module for using the KEGG online
API. This has an equivalent kegg_get function which you could
use as follows:

from Bio.KEGG.REST import kegg_get
from Bio.KEGG import Enzyme
with open("ec:5.4.2.2.txt", "w") as out_handle:
    out_handle.write(kegg_get("ec:5.4.2.2").read())
with open("ec:5.4.2.2.txt") as in_handle:
    records = list(Enzyme.parse(in_handle))
record = records[0]
print(record.classname)
print(record.entry)

Again, the output should be:

['Isomerases;', 'Intramolecular transferases;', 'Phosphotransferases
(phosphomutases)']
5.4.2.2

I've filed an issue to remind us to look at this:
https://github.com/biopython/biopython/issues/592

Peter

On Fri, Aug 7, 2015 at 3:56 AM, ning luwen <bioinformaticsing at gmail.com> wrote:
> Dear All,
>
> I followed the tutorial
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc231 to learn KEGG
> things in biopython, but without lucky, any suggestion?
>
>>>> from Bio import KEGG
>>>> from Bio.KEGG import Enzyme
>>>> request = KEGG.get("ec:5.4.2.2")
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> AttributeError: 'module' object has no attribute 'get'
>>>> import Bio
>>>> print Bio.__version__
> 1.65
>
>
> --
> regards,
> luwen ning
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython