I thought the translation-exon mapping can be solved by "order" or "sort".
Now I think of it, it can not. Thus, I haven't got any examples of the
"ORDER BY" or "SORT BY" requirement.
--jenny
On Tue, Sep 9, 2008 at 2:16 PM, Christopher Lee <[EMAIL PROTECTED]> wrote:
>
> Thanks, Jenny. Do you have any examples of the "ORDER BY" requirement
> that you wanted to add to SQLTable and SQLGraph? None of these
> examples seem to have any ORDER BY or sort() step... or did I miss
> something?
>
> -- Chris
>
>
> On Sep 9, 2008, at 2:06 PM, Jenny Qing Qian wrote:
>
> >
> >
> > On Tue, Sep 9, 2008 at 1:15 PM, Christopher Lee <[EMAIL PROTECTED]>
> > wrote:
> >
> >
> > On Sep 9, 2008, at 1:09 PM, Jenny Qing Qian wrote:
> >
> > > So, for the pygr 0.8 release, will the SQLTable and SQLGraph support
> > > the order of iteration? So that I can implement the one-to-many
> > > relationship between translation and exon properly, as discussed
> > > during the sprint session at Caltech.
> >
> > Yes, let's do it! Probably the best place to start is for you to give
> > me examples of the kinds of code or SQL expressions you are currently
> > having to use to get the results you want, then we can figure out how
> > to make the standard SQLTable and SQLGraph components support that.
> >
> > class Translation(StableObj, BaseModel):
> >
> > def get_all_exons(self):
> > transcript_id = self.transcript_id
> > start_exon_id = self.start_exon_id
> > end_exon_id = self.end_exon_id
> > ...
> > exonAdaptor = coreDBAdaptor.get_adaptor('exon')
> > exons = exonAdaptor.fetch_all_by_translation(transcript_id,
> > start_exon_id, end_exon_id)
> > return exons
> >
> > class ExonAdaptor(FeatureAdaptor):
> >
> > def fetch_all_by_translation(self, transcript_id, start_exon_id,
> > end_exon_id):
> >
> > cursor = self.cursor
> >
> > # get the start_rank for the given transcript_id and the
> > given start_exon_id from the exon_transcript table
> > n = cursor.execute('select rank from %s.exon_transcript
> > where transcript_id = %%s and exon_id = %%s' %(self.db),
> > (transcript_id, start_exon_id))
> > t = cursor.fetchall()
> > if n != 1:
> > raise KeyError('Warning: duplicated!')
> > start_rank = t[0][0]
> >
> > # get the end_rank for the given transcript_id and the given
> > end_exon_id from the exon_transcript table
> > n = cursor.execute('select rank from %s.exon_transcript
> > where transcript_id = %%s and exon_id = %%s' %(self.db),
> > (transcript_id, end_exon_id))
> > t = cursor.fetchall()
> > if n != 1:
> > raise KeyError('Warning: duplicated!')
> > end_rank = t[0][0]
> >
> > # fetch all the exons for the given transcript_id between
> > the start_rank and end_rank inclusive from the exon_transcript table
> > n = cursor.execute('select exon_id from %s.exon_transcript
> > where transcript_id = %%s and rank >= %%s and rank <= %%s' %
> > (self.db), (transcript_id, start_rank, end_rank))
> > t = cursor.fetchall()
> > exons = []
> > if n == 0:
> > return exons
> > for row in t:
> > e = self[row[0]]
> > exons.append(e)
> > return exons
> >
> >
> >
> >
> >
> >
> >
> >
> > >
>
>
> >
>
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