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

[Daniel Hughes]

generally, the most convenient means to i've found to do this for whole
database (10k+ genes/100k+ dna features) in-place transformations is to use
an assembly mapper directly to do the coordinate transformation and then
raw sql to update seq_region_id and positions.

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org



2012/6/28 Fairley, Susan <s.fairley at abdn.ac.uk>

> 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<http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Fe%0Aature.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.
> >>>
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