[ensembl-dev] Chromosome-HGNC mapping

[Andy Yates]

Hi Monica,

Ah I believe there is some confusion to the relationship between a Gene and its GeneAdaptor. Bio::EnsEMBL::Gene provides accessors to a gene's attributes such as start, end & strand (as you've found). GeneAdaptor (http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1GeneAdaptor.html) is responsible for querying the Ensembl database and returning Gene objects. As a user consuming Ensembl data you should query for an object type & use the methods on the object to retrieve data. You may also find the tutorial helpful (http://www.ensembl.org/info/docs/api/core/core_tutorial.html) especially the sections on features, genes, transcripts and exons.

All the best,

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 22 Jul 2013, at 15:44, "Manam, Monica (NIH/NCI) [F]" <monica.manam at nih.gov> wrote:

> I have one last question Andy,
> 
> I do not want to define the start & the ends like the link you gave.
> I want to fetch them.
> 
> However,
> 
> I tried this & it worked :
> ---------------------------
> #!/opt/nasapps/applibs/perl-5.16.2/bin/perl
> 
> 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')};
> 
> foreach(@genes){
> my $gene=shift(@genes);
>    my $gstring = feature2string($gene);
>    print "$gstring\n";
>    }
> 
> 
>    sub feature2string
> {
>    my $feature = shift;
> 
>    my $stable_id  = $feature->stable_id();
>    my $seq_region = $feature->slice->seq_region_name();
>    my $start      = $feature->start();
>    my $end        = $feature->end();
>    my $strand     = $feature->strand();
> 
>    return sprintf( "%s: %s:%d-%d (%+d)",
>        $stable_id, $seq_region, $start, $end, $strand );
> }
> 
> -----------------------
> 
> 
> Output (which I wanted):
> 
> ENSG00000151379: 2:17997763-17998368 (+1)
> 
> -----------------------
> 
> But, thanks for all the help Andy!
> Good day!!
> 
> -- 
> Monica Manam
> Summer Intern
> CCRIFX BioInformatics CORE
> NCI-NIH
> 
> 
> 
> 
> On 7/22/13 10:37 AM, "Andy Yates" <ayates at ebi.ac.uk> wrote:
> 
>> Hi there,
>> 
>> Yes that's what I'm getting. The method is returning you a Gene object.
>> To access Gene attributes you will have to call methods on the object.
>> You can find the full list of available methods from
>> http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1G
>> ene.html.
>> 
>> Hope this helps,
>> 
>> Andy
>> 
>> On 22 Jul 2013, at 15:34, "Manam, Monica (NIH/NCI) [F]"
>> <monica.manam at nih.gov> wrote:
>> 
>>> Im sorry I sent you the prev code, I initially commented out the
>>> "strict"
>>> & "warning" to test & removed the comment while sending it to you.
>>> Thanks, however the result of this command is :
>>> 
>>> 71 at -e line 1.
>>> 
>>> The result of the edited code, with the variable declaration etc is "
>>> 
>>> Bio::EnsEMBL::Gene=HASH(0x303a570)
>>> 
>>> 
>>> Isn't this what you are getting?
>>> 
>>> Thanks,
>>> Monica.
>>> 
>>> 
>>> 
>>> On 7/22/13 10:25 AM, "Andy Yates" <ayates at ebi.ac.uk> wrote:
>>> 
>>>> perl -MBio::EnsEMBL::ApiVersion -e 'warn
>>>> Bio::EnsEMBL::ApiVersion::software_version()'
>>> 
>>> 
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>> 
>> 
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> 
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