[ensembl-dev] update API issue

[Andy Yates]

Hi there,

A reference sequence is detected by the non-existence of a non_ref flag in seq_region_attrib. I've done this query in 73:

select *
from seq_region sr
join seq_region_attrib sra using (seq_region_id)
join attrib_type a using (attrib_type_id)
where sr.name = 'HSCHR6_MHC_MCF_CTG1'
and a.code = 'non_ref'

And have got no rows back suggesting that $gene->slice->is_reference() when slice is HSCHR6_MHC_MCF_CTG1 will return false. Could you send us your code please? 

Andy

On 15 Nov 2013, at 14:26, nconte at ebi.ac.uk wrote:

> Hi,
> I have been updating my ensembl API versions from 71 to 73 today, and
> reran a script to test it was working.
> In my script I am excluding genes  Ids for haplotypes /  LRG /
> pseudoautomosal
> or  assembly patches/fixes regions. I am using this test/method to exclude
> them
> (if $gene->slice->is_reference)
> 
> I am now getting genes mapping on HSCHR6_MHC_MCF_CTG1 which were excluded
> on my last version of the API. Is the slice->is_reference deprecated?
> Thanks
> Nathalie
> 
> 
> 
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