[BioPython] Bioregistry...doesn't work with me

[Jan T. Kim]

On Fri, Apr 01, 2005 at 03:04:15PM +0200, Aur?lie Bornot wrote:
> 
> I am trying to retrieve sequences with the script of the CookBook and it doesn't work...
> I don't understand why....
> Can someone tell me what I did wrong ?

[deleted output of print commands]

> >>> from Bio import db
> >>> print db
> >>> db.keys()
> >>> sp = db["swissprot"]
> >>> sp
> <Bio.config.DBRegistry.DBGroup instance at 0x00ACEB48>
> >>> record_handle = sp['O23729']
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "C:\Python24\lib\site-packages\Bio\config\DBRegistry.py", line 150, in __
> getitem__
>     data = self._run_serial(key)
>   File "C:\Python24\lib\site-packages\Bio\config\DBRegistry.py", line 217, in _r
> un_serial
>     raise KeyError, "I could not get any results."
> KeyError: 'I could not get any results.'
> 
> 
> I have verified : the entry O23729 is still correct....

Your example works for me:
>>> record_handle = sp['O23729']
>>> record_handle
<StringIO.StringIO instance at 0xf66b7c2c>
>>> print record_handle.readline()
ID   CHS3_BROFI     STANDARD;      PRT;   394 AA.

>>> print record_handle.readline()
AC   O23729;

>>> print record_handle.readline()
DT   15-JUL-1999 (Rel. 38, Created)

> I must work with Windows XP, may the problem comes from this...?

That's always a possiblility (I've tried on Linux), but it's more likely
a network problem, Biopython may have been unable to get the record
because e.g.

    * you are behind some firewall that doesn't allow the kind of http
      used by Biopython for retrieving the record

    * the network connectivity between your site and www.expasy.ch
      may have been transiently down

Best regards, Jan
-- 
 +- Jan T. Kim -------------------------------------------------------+
 |    *NEW*    email: jtk at cmp.uea.ac.uk                               |
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