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.<br>
<br>dan.<br><br clear="all"><br clear="all">Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)<br>-------------------------------------------------------------------------------------<br><a href="mailto:dsth@cantab.net">dsth@cantab.net</a><br>
<a href="mailto:dsth@cpan.org">dsth@cpan.org</a><br>
<br>
<br><br><div class="gmail_quote">2012/6/28 Fairley, Susan <span dir="ltr"><<a href="mailto:s.fairley@abdn.ac.uk" target="_blank">s.fairley@abdn.ac.uk</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Dan,<br>
<br>
Depending on your purposes, it could also be worth considering transform.<br>
<br>
<a href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Fe%0Aature.html#a6691fe33ab10ee3c70c1a1213d030fc2" target="_blank">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Fe<br>
ature.html#a6691fe33ab10ee3c70c1a1213d030fc2</a><br>
<br>
Regards,<br>
Susan.<br>
<div><div class="h5"><br>
On 28/06/2012 09:55, "Dan Bolser" <<a href="mailto:dbolser@ebi.ac.uk">dbolser@ebi.ac.uk</a>> wrote:<br>
<br>
>Many thanks Andrew,<br>
><br>
>Looks like a very useful script!<br>
><br>
>Actually, I was after something simpler, a way to move features<br>
>between coordinate systems _within_ one assembly. I haven't started to<br>
>try to code this yet (looking for something ready made first), but<br>
>hopefully the 'hard' part is just plumbing in command line options [1]<br>
>to a project call [2] over the selected features.<br>
><br>
><br>
>Cheers,<br>
>Dan.<br>
><br>
>[1]<br>
><a href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1U" target="_blank">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1U</a><br>
>tils_1_1CliHelper.html<br>
>[2]<br>
><a href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1F" target="_blank">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1F</a><br>
>eature.html#a53cf34cc3eefdeddc959ba395462bc50<br>
><br>
>On 27 June 2012 20:32, Olson, Andrew <<a href="mailto:olson@cshl.edu">olson@cshl.edu</a>> wrote:<br>
>> Hi Dan,<br>
>> I have a general purpose script that I've used to map features in bulk<br>
>>from one assembly to another. It operates on tab delimited files (like<br>
>>from mysqldump) and uses a mapping file to guide the projection. This<br>
>>lets you project features on many tables and then import the new tables<br>
>>to another core database. One warning though, it doesn't require the<br>
>>start and end coordinates of a feature to be the same distance apart,<br>
>>but this check can be added at about line 36 if needed.<br>
>> Andrew<br>
>><br>
>> On Jun 27, 2012, at 1:58 PM, Dan Bolser wrote:<br>
>><br>
>>> Does anyone have a a 'general' (type agnostic) feature 'projection'<br>
>>> script? i.e. a script that will project all features to toplevel, or<br>
>>> feature type x from level y to level z in a given core database?<br>
>>><br>
>>> Cheers,<br>
>>> Dan.<br>
>>><br>
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>><br>
>><br>
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