[ensembl-dev] Chromosome list

[Toni Hermoso Pulido]

Yes, this works for me.

I'll adapt my scripts.

Thanks for replying so fast!

Al 01/10/13 17:20, En/na Anne Parker ha escrit:
> 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?
>>

-- 
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