[ensembl-dev] Is this feature on a patch

[Jay Humphrey]

Thanks, that helps! In API terms: feature->slice->get_all_Attributes

On 30/01/2013 16:44, Fairley, Susan wrote:
> Hi Jay,
>
> The patch seq_regions are identifiable using seq_region_attrib (the same
> mechanism that, for example, identifies toplevel seq_regions).
>
> There are two different attribs - one for novel patches and one for fix
> patches.
>
> mysql> select * from attrib_type where attrib_type_id in (312,313);
> +----------------+-------------+----------------------+--------------------
> ---------------------------------------------------------------------------
> --------------------------------------------+
> | attrib_type_id | code        | name                 | description
>
>                                              |
> +----------------+-------------+----------------------+--------------------
> ---------------------------------------------------------------------------
> --------------------------------------------+
> |            312 | patch_fix   | Assembly Patch Fix   | Assembly patch
> that will, in the next assembly release, replace the corresponding
> sequence found in the current assembly                  |
> |            313 | patch_novel | Assembly Patch Novel | Assembly patch
> that will, in the next assembly release, be retained as an alternate
> non-reference sequence in a similar way to haplotypes |
> +----------------+-------------+----------------------+--------------------
> ---------------------------------------------------------------------------
> --------------------------------------------+
> 2 rows in set (0.01 sec)
>
> Checking for those in seq_region_attrib should identify the patches.
>
> Hope that helps,
> Susan.
>
>
>
> On 30/01/2013 16:21, "Jay Humphrey" <jhumphre at ebi.ac.uk> wrote:
>
>> A little more info:
>> The coord systems for these are all name, rank, version = chromosome, 1,
>> GRCh37.
>> Perhaps one of these (rank?) could be changed in the database without
>> impacting other areas?
>>
>> On 30/01/2013 16:10, Jay Humphrey wrote:
>>> In a list of genes and transcripts I want to discard the ones on a
>>> patch contig. Is there any way to tell it's a patch besides the name?
>>> Examples showing stable id: seq_region_name
>>>
>>> ENSG00000263007: HG388_HG400_PATCH
>>> ENSG00000109846: 11
>>> ENST00000574550: HG388_HG400_PATCH
>>> ENST00000526180: 11
>>>
>> --
>> Jay Humphrey                   Ensembl Genomes Web Developer
>> EMBL-EBI                       Tel: +44-(0)1223-492682
>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>>
>>
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>
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-- 
Jay Humphrey                   Ensembl Genomes Web Developer
EMBL-EBI                       Tel: +44-(0)1223-492682
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/