[ensembl-dev] Chromosome-HGNC mapping

[Andy Yates]

Hi Monica

Could you post your script please along with the version of ensembl you are attempting to use & database version. The error you are receiving points towards using a more recent version of the Api with an older database

Andy

Sent from my mobile.

On 19 Jul 2013, at 20:51, "Manam, Monica (NIH/NCI) [F]" <monica.manam at nih.gov> wrote:

> Hello Emily,
> 
> I am getting an exception when I tried using the code like this:
> 
> my $gene_adaptor = $dbCore->get_GeneAdaptor();
> 
> my  $va_adaptor->fetch_all_by_external_name("BCRA2");
> 
> 
> 
> Exception :
> 
> DBD::mysql::st execute failed: Unknown column 'species_id' in 'where
> clause' at 
> /opt/nasapps/development/ensembl-api/ensembl/modules//Bio/EnsEMBL/DBSQL/Bas
> eMetaContainer.pm line 130.
> 
> Do you know why?
> 
> 
> Thanks,
> -- 
> Monica Manam
> 
> CCRIFX BioInformatics CORE
> NCI-NIH
> 
> 
> 
> On 7/19/13 4:06 AM, "Emily Pritchard" <emily at ebi.ac.uk> wrote:
> 
>> Hi Monica
>> 
>> Yes, you can do that.
>> 
>> Use fetch_by_external_id in the gene_adaptor module to get genes from
>> our database using HGNC or RefSeq IDs:
>> http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1D
>> BSQL_1_1GeneAdaptor.html#a940d6dc7e9273ad373a23eb563a455e6
>> 
>> Then you can use commands from the Gene module to get various bits of
>> information:
>> http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1G
>> ene.html
>> 
>> You may wish to use seq_region_name, seq_region_start and seq_region_end
>> to get coordinates, while get_all_Exons and get_all_Transcripts will
>> give you exons and transcripts respectively.
>> 
>> Hope this helps
>> 
>> Emily
>> Ensembl Outreach
>> 
>> 
>> On 18/07/2013 19:30, Manam, Monica (NIH/NCI) [F] wrote:
>>> Hello Team,
>>> 
>>> I have a question regarding the API which gives the Gene & it's
>>> attributes mapping.
>>> For a given HGNC/RefSeq Id , can we get the chromosome name & its start
>>> & end , transcript , exon , & gene information?
>>> 
>>> I know the API under "Genes, Transcripts, and Exons" to get the gene
>>> data, & it takes the chromosome number, start & end as input.
>>> 
>>> Thanks ,
>>> --
>>> Monica Manam
>>> CCRIFX BioInformatics CORE
>>> NCI-NIH
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
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>> 
>> -- 
>> Dr Emily Pritchard
>> Ensembl Outreach Officer
>> 
>> EMBL - European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge
>> CB10 1SD
>> UK
>> 
>> 
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> 
> 
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