[ensembl-dev] how to get genes from unplaced scaffolds via Perl API

Will Chow wc2 at sanger.ac.uk
Tue Sep 4 15:27:53 BST 2012


Javier is right,  you can use top-level.  I thought it might return more than the advertised 22 unplaced, but I might be just looking at the wrong query.

mysql> select coord_system.name, coord_system_id, count(*) from seq_region inner join seq_region_attrib using (seq_region_id) inner join coord_system using (coord_system_id) where attrib_type_id = 6 group by coord_system_id;
+------------+-----------------+----------+
| name       | coord_system_id | count(*) |
+------------+-----------------+----------+
| scaffold   |               2 |       44 | 
| chromosome |               3 |       22 | 
+------------+-----------------+----------+
2 rows in set (0.00 sec)


All the best,

Will





On 4 Sep 2012, at 15:11, Javier Herrero wrote:

> Dear Sergei
> 
> You can use
> 
> my @slices = @{ $slice_adaptor->fetch_all('toplevel') };
> 
> instead. The coordinate system alias "toplevel" corresponds to all the so-called top-level sequences, i.e. the chromosomes (if any) and all the unplaced scaffolds.
> 
> I hope this helps
> 
> Javier
> 
> On 01/09/12 07:58, Sergei Manakov wrote:
>> Hello,
>> 
>> According to GRCm38 description there are 21 chromosomes and 22
>> unplaced scaffolds this version of the mouse genome.
>> 
>> How can I get slices for these unplaced scaffolds?
>> 
>> this doesn't work:
>> 
>> my @slices = @{ $slice_adaptor->fetch_all('chromosome') };
>> 
>> 
>> thanks very much!
>> Sergei
>> 
>> 
>> 
>> 
>> 
> 
> -- 
> Javier Herrero, PhD
> Ensembl Coordinator and Ensembl Compara Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
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