[BioPython] Re: [BioSQL-l] python

[Hilmar Lapp]

Christen, I'm afraid there aren't too many python-savvy people on the 
biosql list. I forwarded your email to the biopython folks, hoping that 
they can help you better.

	-hilmar

On Monday, December 8, 2003, at 05:57  AM, christen wrote:

> Hi there
>
> I am a new comer to python and biosql
>
> I have tried to get working biosql under mysql and python as ewplained 
> in
> Basic BioSQL with Biopoython
> I have donwloaded the latest version of both, and tried the example 
> with
> cor6_6.gb
>
> then I got numerous problems
>
> I fixed the first one by changing line 104 in cursors from
>             if args is None:
> to :
>             if args is None or args=='':
>
> then in Loader, in def _load_reference(self, reference, rank, 
> bioentry_id):,
> i made the following changes (in particular replaced JOIN by INNER 
> JOIN)
> if reference.medline_id:
>             sql="SELECT reference_id" \
>                 "  FROM reference INNER JOIN dbxref ON reference 
> .dbxref_id
> = dbxref.dbxref_id" \
>                 " WHERE ((dbname = 'MEDLINE') AND (accession = %s))"
>             refs =
> self.adaptor.execute_and_fetch_col0(sql,reference.medline_id)
>
>
> Now, I have one more pb:
>
> Traceback (most recent call last):
>   File "C:\Python23\RC_databases\rc_BioSQL_GenBank.py", line 21,
> in -toplevel-
>     db.load(iterator)
>   File "C:\Python23\lib\site-packages\BioSQL\BioSeqDatabase.py", line 
> 343,
> in load
>     db_loader.load_seqrecord(cur_record)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 46, in
> load_seqrecord
>     self._load_seqfeature(seq_feature, seq_feature_num, bioentry_id)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 366, in
> _load_seqfeature
>     self._load_seqfeature_locations(feature, seqfeature_id)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 409, in
> _load_seqfeature_locations
>     self._insert_seqfeature_location(feature, 1, seqfeature_id)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 430, in
> _insert_seqfeature_location
>     self.adaptor.execute(sql, (seqfeature_id, start, end, strand, 
> rank))
>   File "C:\Python23\lib\site-packages\BioSQL\BioSeqDatabase.py", line 
> 223,
> in execute
>     self.cursor.execute(sql, args)
>   File "C:\Python23\lib\site-packages\MySQLdb\cursors.py", line 95, in
> execute
>     return self._execute(query, args)
>   File "C:\Python23\lib\site-packages\MySQLdb\cursors.py", line 119, in
> _execute
>     self.errorhandler(self, exc, value)
>   File "C:\Python23\Lib\site-packages\MySQLdb\connections.py", line 
> 33, in
> defaulterrorhandler
>     raise errorclass, errorvalue
> OperationalError: (1048, "Le champ 'strand' ne peut \xeatre vide 
> (null)")
>
>
> I am for the time being only trying some quick and dirty (like 
> modification
> of cursor instead of loader I guess...) changes  to try to get it 
> working
> My questions are :
> Is there somebody else having trouble, or do you I miss something ?
> If I did it right, Is there somebody else trying to fix these problems 
> ?
> If things need some help, it would be very nice to have some clear
> description of biosql structure. I have not been able to find it. 
> Somebody
> could help ?
>
> thanks in advance
>
>
>
>
>
> Richard CHRISTEN
> Champion de saut en largeur
> UMR6543 CNRS - Université de Nice Sophia Antipolis
>
> Centre de Biochimie
> Parc Valrose
> 06108 Nice cedex2
>
> tel  33 - 492 076 947
> fax 33 - 492 076 408
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------