[ensembl-dev] coord system

[Bronwen Aken]

Hi Gary,

Do you have the correct meta_value for your meta key 'assembly.mapping'?

If we take cow as an example, first look at the name and version columns in the coord_system table:

mysql -uanonymous -hensembldb.ensembl.org -P5306 -Dbos_taurus_core_61_4j -e "select * from coord_system"
+-----------------+------------+------------+----------+------+--------------------------------+
| coord_system_id | species_id | name       | version  | rank | attrib                         |
+-----------------+------------+------------+----------+------+--------------------------------+
|               1 |          1 | contig     | Btau_4.0 |    2 | default_version,sequence_level |
|               2 |          1 | chromosome | Btau_4.0 |    1 | default_version                |
+-----------------+------------+------------+----------+------+--------------------------------+

There should be a mapping in the meta table between chromosome and contig:

mysql -uanonymous -hensembldb.ensembl.org -P5306 -Dbos_taurus_core_61_4j -e "select * from meta where meta_key = 'assembly.mapping'"
+---------+------------+------------------+-------------------------------------+
| meta_id | species_id | meta_key         | meta_value                          |
+---------+------------+------------------+-------------------------------------+
|      26 |          1 | assembly.mapping | chromosome:Btau_4.0|contig:Btau_4.0 |
+---------+------------+------------------+-------------------------------------+

The meta_value has the format:
$coord_system_name1.":".$coord_system_version1."|".$coord_system_name2.":".$coord_system_version2
eg "chromosome:dictybase.01|contig:dictybase.01"

Cheers,
Bronwen


On 13 Mar 2011, at 17:13, Gary Duncan wrote:

> Help
> What do I need to do to fix this?
> attached is the code I am new to the api?
> you want hurt my feelings if its some simple.
> 
> thanks in advance
> -------------------- WARNING ----------------------
> MSG: Using implicit mapping path between 'chromosome:dictybase.01' and 'contig:dictybase.01' coord systems.
> An explicit 'assembly.mapping' entry should be added to the meta table.
> Example: 'chromosome:dictybase.01|supercontig:dictybase.01|contig:dictybase.01'
> 
> FILE: EnsEMBL/DBSQL/CoordSystemAdaptor.pm LINE: 708
> CALLED BY: EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm  LINE: 222
> Ensembl API version = 61
> ---------------------------------------------------
> 
> 
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