[ensembl-dev] Projecting features

Dan Bolser dbolser at ebi.ac.uk
Tue Jan 15 14:33:48 GMT 2013


Many thanks Daniel,

Following through this example, I thought I had found my error, namely
the update method needs to be called on the adaptor, not the feature
object... Unfortunately, I now get more bugs, but I'll try to resolve
them.


Thanks all,
Dan.

On 15 January 2013 14:13, Daniel Barrell <db8 at sanger.ac.uk> wrote:
>
> Hi Dan,
>
> You could look at the transform example in:
>
> /ensembl-analysis/scripts/genebuild/copy_genes.pl
>
> I've used this script in the past to transfer genes between coordinate
> systems.
>
> Daniel
>
>
>
> On 15/01/13 13:54, Dan Bolser wrote:
>>
>> Have you got code examples?
>>
>> Currently I may just dump TSV for SQL UPDATE...
>>
>>
>> On 15 January 2013 13:43, Andreas Kusalananda Kähäri<ak4 at sanger.ac.uk>
>> wrote:
>>>
>>> Hi,
>>>
>>> During the gene build process we regularly modify built models in bulk,
>>> but never using update() AFAIK.  Instead the results of a pipeline step
>>> is written to a new (empty) database.  The final database that we hand
>>> over for the release is created by copying data from a few of these
>>> result databases.  This way it's easy to go back to a previous step and
>>> rerun from there with modified parameters/code.
>>>
>>> Cheers,
>>> Andreas
>>>
>>>
>>> On Tue, Jan 15, 2013 at 01:03:12PM +0000, Kieron Taylor wrote:
>>>>
>>>> Hi Dan, this is trickier than you might like.
>>>>
>>>> In general, database changes are made in response to ->store() or
>>>> ->update() methods on adaptors. update() calls may not change every aspect
>>>> of the object. I suspect update() will not have the desired effect on all
>>>> Features, but you should investigate this yourself.
>>>>
>>>> The problem with using store is the issue of storing the same Feature
>>>> again, but with new coordinates. This will probably trigger parts of the
>>>> code that prevent the storing of the same Feature twice, or else give you
>>>> two copies with slight differences. You may need to resort to ->remove(),
>>>> and the internal db identifiers will change...
>>>>
>>>> In summary, tread lightly and verify your results before you unleash the
>>>> script.
>>>>
>>>> Kieron
>>>>
>>>> On 15 Jan 2013, at 11:36, Dan Bolser wrote:
>>>>
>>>>> I wrote a script to project features from contigs to chromosomes using
>>>>> the transform method.
>>>>>
>>>>> https://gist.github.com/4537997
>>>>>
>>>>>
>>>>> Once I have the projected feature, I try to update the database by
>>>>> calling (line 73):
>>>>>
>>>>> $ff->slice( $ffp->slice );
>>>>>
>>>>>
>>>>> however, this doesn't update the database with the new feature
>>>>> coordinates.
>>>>>
>>>>> Is there a method I need to call to update the feature in the database?
>>>>>
>>>>>
>>>>> Cheers,
>>>>> Dan.
>>>>>
>>>>> _______________________________________________
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>>>>
>>>> Kieron Taylor PhD.
>>>> Ensembl Core software developer
>>>>
>>>> EMBL - European Bioinformatics Institute
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>> --
>>> Andreas Kusalananda Kähäri
>>> Ensembl Gene Annotation Team
>>>
>>> Tap tap tap.
>>>
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>
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