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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