[BioPython] [BioSQL-l] update DBSeqRecords

[Hilmar Lapp]

Andreas -

I really don't know anything about Biopython (but many others on the  
list may, especially the Biopython list, which I'm cc'ing too).

So - I'm passing this on to Biopythonians to respond.

	-hilmar

On Feb 14, 2008, at 1:52 AM, Andreas De Stefani wrote:

> Thanks Hilmar,
>
> I kind of figured this and i am just using the adaptor to execute  
> the sql statement to delete the entry.
> I also noticed that i cannot access all the information via  
> biopython/biosql, i would like to show the comments for each entry  
> but i cant find any attribute in the DBSeqRecord to access this  
> information. Is this something which will be added in the near future?
>
> My workaround is to use the adaptor from the record and just  
> execute a sql query ... but that might not be the ideal way to do it!?
>
> thanks again,
>
> Andreas
>
>
>
> Hilmar Lapp wrote:
>> As Peter says this is easily possible, simply delete the sequence  
>> (protein) first that you want to update and then reload it.
>>
>> This is also called the 'refresh' mode of updating.
>>
>>     -hilmar
>>
>> On Feb 13, 2008, at 6:39 PM, Andreas De Stefani wrote:
>>
>>> Hi Guys,
>>>
>>> I was wondering if it is possible to update a single DBSeqRecord,  
>>> without having to delete the whole sub datbase first...
>>>
>>> I am using BioPython and BioSQL and what I intend todo is to  
>>> create a local "cache" for protein informations which i get from  
>>> the web, and after a month or so i would like to re-fetch the  
>>> info from the web and update the local protein information  
>>> "cache" (which uses BioSQL).
>>>
>>> It basically will work like this:
>>>
>>> if the user requests information for a certain protein the  
>>> program queries the local DB using the accession number and sees  
>>> if there is information about the protein, if not (or if the  
>>> protein is expired, ie older than a month) it gets the info from  
>>> the web (expasy) and loads (updates the protein information in)  
>>> the local database. However, is a update of a single protein  
>>> entry possible? when inserting the same protein i get the  
>>> following error:
>>>
>>> (<class '_mysql_exceptions.IntegrityError'>, IntegrityError(1062,  
>>> "Duplicate entry 'P08317-1-0' for key 2"), <traceback object at  
>>> 0xd6b170>)
>>>
>>> i am just using db.load(...) again, but maybe there is another  
>>> way to update entries?
>>>
>>> Hope somebody can help me with this, thanks very much in advance!
>>>
>>> Andy
>>> _______________________________________________
>>> BioSQL-l mailing list
>>> BioSQL-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>
>
>
> -- 
> Biontrack - bioinformatics solutions
> e: andreas.destefani at biontrack.com
> w: www.biontrack.com
> t: +353 (0)1 716 3760
> f: +353 (0)1 716 3709
> m: +353 85 141 9941

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================