[ensembl-dev] Exporting regions

Stefan Kirov stefan.kirov at bms.com
Mon Sep 10 17:52:04 BST 2012


Thanks a lot Andy! That makes sense...
If this is not too much to ask for- in some of the next 
releases could you include data on how to convert the 
sub-slice to the larger contig/slice? Perhaps as a note in 
the source feature.... Just in case you have too much free 
time on your hands ;-) .
Cheers!
Stefan

On 09/10/2012 10:52 AM, Andy Yates wrote:
> Hi Stefan,
>
> This is because the coordinates given in the Genbank files are relative to the slice you requested and the numbering is relative to that sub-slice. Those attributes which refer to other contigs are the elements which extend beyond the bounds of the requested slice e.g.
>
> http://www.ensembl.org/Homo_sapiens/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=genbank;r=6:133017695-133161157;strand=feature;param=similarity;param=repeat;param=genscan;param=contig;param=variation;param=marker;param=gene;param=vegagene;param=estgene;_format=Text
>
> Will return a set of features from VNN1 which starts upstream of the region 6:133017695-133161157. Compare this to a very gene specific subslice e.g. VNN3 at 6:133043926-133055904:
>
> http://www.ensembl.org/Homo_sapiens/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;g=ENSG00000093134;output=genbank;r=6:133043926-133055904;strand=feature;param=similarity;param=repeat;param=genscan;param=contig;param=variation;param=marker;param=gene;param=vegagene;param=estgene;_format=Text
>
> This will contain no coordinates referring to other slices but feature locations will be relative to the requested slice i.e. the Gene location for VNN3 is "complement(1..11979)" and not "complement(133043926..133055904)".
>
> Hope this helps,
>
> Andy
>
> Andrew Yates                   Ensembl Core Software Project Leader
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensembl.org/
>
> On 10 Sep 2012, at 03:45, Stefan Kirov wrote:
>
>> Guys,
>> When exporting genbank for a region I see things like that:
>>
>>      misc_RNA        join(complement(AC009121.8:51066..51103),
>>                      complement(AC009121.8:46967..47862))
>>
>> I was under the impression that the coordinates for any feature would be based on the coordinate system used to export, not a contig based coordinate system.
>> To make things worse sometimes it seems that the coordinate system is the exported slice and sometimes it is mixed.
>> Is this the expected behavior or a bug?
>> Thanks!
>> Stefan
>>
>>
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