[ensembl-dev] Urgent information to extract the refseq_mrna and HGNC symbol for given gene from ENSEMBL

[Magali]

Hi Monica,

In your script, you are trying to call two methods which do not exist,
refseq_mrna and hgnc_symbol.
Unless these have been defined later in your script, we do not have a
direct method in ensembl to do this.

HGNC symbols and Refseq mRNAs are attached to a gene object as an
external reference.
Via the API, these can be accesses using the get_all_DBLinks method.

For example, to get the hgnc symbol of a gene object, you could do the
following:

    my $hgnc_xrefs = $gene->get_all_DBLinks('HGNC');
    foreach my $xref (@$hgnc_xrefs) {
        print $xref->display_id . "\n";
    }

The same would work for RefSeq mRNAs

    my $refseq_xrefs = $gene->get_all_DBLinks('Refseq_mRNA');
    foreach my $xref (@$refseq_xrefs) {
        print $xref->display_id . "\n";
    }


On a side note, in your script you set a logic_name 'refseq_human_import'.
If you want to restrict your study to that specific logic_name, you can
specify it when fetching genes

    my $genes = $slice->get_all_Genes($logic_name);

Do bear in mind though that the gene models from the refseq_human_import
analysis are in the otherfeatures database for human, not in the core one.
Hence, you would need to change your adaptor call

    my $slice_adaptor = $registry->get_adaptor('Human', 'otherfeatures',
    'Slice');


Hope that helps.


Regards,
Magali

On 25/06/13 13:12, Manam, Monica (NIH/NCI) [F] wrote:
> Hello Dev Team !
>
> The API version used is 71.
>
> I am an intern at the NIH(National Institutes Of health), Bethesda. I am working on a project & I need the ensembl API to extract the ref_seq mrna & HGNC symbol for a given gene .
>
> I tried to use the following but got no results, I was getting an exception
>
> "refseq_mrna not known " :
>
>
>
> 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 );
>
>
> }
>
> my $logic_name= 'refseq_human_import';
>
>
> my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' );
>
> my $slice = $slice_adaptor->fetch_by_region( 'chromosome', '2',17997763,17998368);
>
>
> my $genes = $slice->get_all_Genes();
>
> while ( my $gene = shift @{$genes} ) {
>
>     my $gstring = feature2string($gene);
>
>     print "$gstring\n";
>
>
>
>
>  my $transcripts = $gene->get_all_Transcripts();
>
>     while ( my $transcript = shift @{$transcripts} ) {
>
>         my $tstring = feature2string($transcript);
>
>         print "\t$tstring\n";
>
>         print $logic_name."\tGene_biotype=".$gene->biotype.
>
>             "\tTranscript_name=".$transcript->stable_id."\tTranscript_biotype=".$transcript->biotype."\n";
>
>        print $logic_name."\tGene_refseq=".$gene->refseq_mrna."\n";
>
>
>  print $logic_name."\tGene_hgnc=".$gene->hgnc_symbol."\n";
>
>
> Could you kindly help me with this, asap. As this is a time constrained project.
>
>
> Thanks,
>
> Monica Manam
>
> NIH- Intern 2013
>
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