[ensembl-dev] General feature 'projection' script?

[Fairley, Susan]

Hi Dan,

Depending on your purposes, it could also be worth considering transform.

http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Fe
ature.html#a6691fe33ab10ee3c70c1a1213d030fc2

Regards,
Susan.

On 28/06/2012 09:55, "Dan Bolser" <dbolser at ebi.ac.uk> wrote:

>Many thanks Andrew,
>
>Looks like a very useful script!
>
>Actually, I was after something simpler, a way to move features
>between coordinate systems _within_ one assembly. I haven't started to
>try to code this yet (looking for something ready made first), but
>hopefully the 'hard' part is just plumbing in command line options [1]
>to a project call [2] over the selected features.
>
>
>Cheers,
>Dan.
>
>[1]
>http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1U
>tils_1_1CliHelper.html
>[2]
>http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1F
>eature.html#a53cf34cc3eefdeddc959ba395462bc50
>
>On 27 June 2012 20:32, Olson, Andrew <olson at cshl.edu> wrote:
>> Hi Dan,
>> I have a general purpose script that I've used to map features in bulk
>>from one assembly to another.  It operates on tab delimited files (like
>>from mysqldump) and uses a mapping file to guide the projection.  This
>>lets you project features on many tables and then import the new tables
>>to another core database.  One warning though, it doesn't require the
>>start and end coordinates of a feature to be the same distance apart,
>>but this check can be added at about line 36 if needed.
>> Andrew
>>
>> On Jun 27, 2012, at 1:58 PM, Dan Bolser wrote:
>>
>>> Does anyone have a a 'general' (type agnostic) feature 'projection'
>>> script? i.e. a script that will project all features to toplevel, or
>>> feature type x from level y to level z in a given core database?
>>>
>>> Cheers,
>>> Dan.
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> List admin (including subscribe/unsubscribe):
>>>http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe):
>>http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>
>_______________________________________________
>Dev mailing list    Dev at ensembl.org
>List admin (including subscribe/unsubscribe):
>http://lists.ensembl.org/mailman/listinfo/dev
>Ensembl Blog: http://www.ensembl.info/



The University of Aberdeen is a charity registered in Scotland, No SC013683.