[ensembl-dev] problem importing GenBank file into local core DB

[梁薰文]

Hi Dan,

I think we find the "origin-spanning" feature you mentioned. 

The main problem is that we did not set sequence as circular before passing in annotation information. The objects and slice seems to be fine.

Thus, some changes were made and it was successfully stored into core db.

However, we met several problems when withdrawing data from db, such as the wrong recording of “seq_region_start" and “seq_region_end" in gene table. 

Before asking your help, we would like to look into those first.

Thanks very much for your kind help. 

 Susan.


> Dan Staines <dstaines at ebi.ac.uk> 於 2016年7月12日 上午1:26 寫道：
> 
> I'm afraid its not clear from your code what coordinates you are using for your exons, transcripts and genes in the case of a problematic gene. Can you please show exactly what coordinates are being used in each case and how they are being passed to the Exon and Transcript objects?
> 
> Also, can you please share how you are creating the seq_regions/slices to which the genes are attached as this is also important.
> 
> Thanks,
> 
> Dan.
> 
> -- 
> Dan Staines, PhD
> Genomics Technology Infrastructure Coordinator
> EMBL-EBI, Wellcome Trust Genome Campus
> Cambridge CB10 1SD, UK
> Tel: +44-(0)1223-492507
> 
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