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

Manam, Monica (NIH/NCI) [F] monica.manam at nih.gov
Tue Jun 25 13:12:00 BST 2013


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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