[BioPython] Does anyone use EZRetrieve?

[Bruce Southey]

Peter wrote:
> On Thu, Nov 20, 2008 at 8:53 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>   
>> On Thu, Nov 20, 2008 at 8:46 PM, Bruce Southey <bsouthey at gmail.com> wrote:
>>     
>>> Hi,
>>> Does anyone use EZRetrieve
>>> (http://siriusb.umdnj.edu:18080/EZRetrieve/single_r.jsp) ?
>>> This allows a user to retrieve a human, mouse or rat genome nucleic sequence
>>> based on an valid identifier.
>>>
>>> I think that most of the functionality of Bio.EZRetrieve is already present
>>> in Biopython and the genome sources appear to be 5 years old. For example,
>>> it uses LocusLink that was discontinued March 2005.
>>>
>>> If so could you please let me know?
>>>       
>> Actually - could you let the whole mailing list know?  ;)
>>
>> Given nature of the database and the limited functionality this python
>> code offers, if no-one is using Bio.EZRetrieve then it could be
>> considered for deprecation.
>>     
>
> I've seen no replies so I've marked Bio.EZRetrieve as obsolete in CVS
> (and therefore for Biopython 1.50), and unless anyone speaks up it
> will be deprecated in the release after that.
>
> I'm not sure that the EZRetrieve data is that out of date (they may
> have updated things since Bruce looked), but all the Bio.EZRetrieve
> code does is fetch an HTML page and extract the FASTA formatted
> sequence (ignoring any metadata or cross references).  In any case,
> this kind of HTML "screen scraping" is fragile (liable to break when
> the site gets a visual redesign) and is not explicitly condoned by the
> service itself.
>
> Peter
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>   
Hi,
I got nothing back from this nor for Bio.Affy and Bio.NMR (I tried a 
couple of emails) so I would suggest you also mark these as depreciated 
for Biopython 1.5.

The EZRetrieve help page still refers to 2003 releases.
http://siriusb.umdnj.edu:18080/EZRetrieve/help.jsp

Thanks
Bruce