[ensembl-dev] Chromosome-HGNC mapping

[Andy Yates]

Hi Monica,

I have just run your script and found a number of errors in variable declaration and statement termination. However once these were fixed the script ran perfectly fine against my local 71 API. Could you send back the output of the following command:

perl -MBio::EnsEMBL::ApiVersion -e 'warn Bio::EnsEMBL::ApiVersion::software_version()'

Also here is your fixed script:

########################################
use strict;
use warnings;
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
   -host => 'ensembldb.ensembl.org',
   # -host => 'useastdb.ensembl.org',
   -user => 'anonymous'
);
my $gene_adaptor =Bio::EnsEMBL::Registry->get_adaptor( "human", "core","gene" );
my @genes = @{$gene_adaptor->fetch_all_by_external_name('MSGN1')};
print "$genes[0]\n";
########################################

Andy

On 22 Jul 2013, at 15:13, "Manam, Monica (NIH/NCI) [F]" <monica.manam at nih.gov> wrote:

> Hi andy,
> 
> I am using the below:
> The API version is 71.
> --------------
> use strict;
> use warnings;
> 
> use Bio::EnsEMBL::Registry;
> 
> my $registry = 'Bio::EnsEMBL::Registry';
> 
> $registry->load_registry_from_db(
>    -host => 'ensembldb.ensembl.org', # alternatively
> 'useastdb.ensembl.org'
>    -user => 'anonymous'
> );
> 
> 
> $gene_adaptor =Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
> "gene" );
> 
> @genes = @{$gene_adaptor->fetch_all_by_external_name('MSGN1')}
> 
> print "$genes[0]\n";
> 
> --------------
> 
> 
> I am not able to fetch any valid values form the DB related to MSGN1 , I
> want to get its Gene information.
> 
> Thanks,
> Monica. 
> 
> On 7/19/13 6:06 PM, "Andy Yates" <ayates at ebi.ac.uk> wrote:
> 
>> 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/B
>>> as
>>> 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
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Dev mailing list    Dev at ensembl.org
>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>> Ensembl Blog: http://www.ensembl.info/
>>>> 
>>>> -- 
>>>> 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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>> 
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> 
> 
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