[ensembl-dev] Projecting features

[Daniel Barrell]

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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