[ensembl-dev] Exporting regions

[Andy Yates]

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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