[ensembl-dev] Chromosome list

[Anne Parker]

Hi Toni

We recently switched over to storing the chromosome list in the core database, which we currently retrieve with this SQL:

select s.name 
      from seq_region s, seq_region_attrib sa, attrib_type a 
      where sa.seq_region_id = s.seq_region_id 
        and sa.attrib_type_id = a.attrib_type_id 
        and a.code = "karyotype_rank" 
      order by abs(sa.value);

for web purposes. 

Is this the kind of thing you're looking for?

Cheers

Anne



On 10 Jan 2013, at 16:13, Toni Hermoso Pulido <toni.hermoso at crg.cat> wrote:

> Hello,
> 
> I asked about chromosomes list some months ago:
> http://lists.ensembl.org/pipermail/dev/2012-June/007652.html
> and, in the end, I've been using ini files for having a list of chromosomes:
> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/public-plugins/ensembl/conf/ini-files/?root=ensembl
> 
> However, I noticed that in version 69, ENSEMBL_CHROMOSOMES paramater got commented -> 'preceding ;'
> Example here: http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/public-plugins/ensembl/conf/ini-files/Bos_taurus.ini?revision=1.92&root=ensembl&view=markup
> 
> Does it mean that this listing will not be 'reliable' anymore?
> If so, which should be the preferable way to follow to get that information from now on?
> 
> Cheers,
> -- 
> Toni Hermoso Pulido
> Bioinformatician
> 
> Bioinformatics Core Facility
> http://biocore.crg.cat
> CRG - Centre de Regulació Genòmica (Room 439)
> Parc de Recerca Biomèdica de Barcelona (PRBB)
> Doctor Aiguader, 88
> 08003 Barcelona
> 
> toni.hermoso at crg.cat
> Phone: +34 93 316 02 02
> 
> 
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Anne Parker
Ensembl Web Production Manager
http://www.ensembl.org