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Hi Monica,<br>
<br>
In your script, you are trying to call two methods which do not
exist, refseq_mrna and hgnc_symbol.<br>
Unless these have been defined later in your script, we do not have
a direct method in ensembl to do this.<br>
<br>
HGNC symbols and Refseq mRNAs are attached to a gene object as an
external reference.<br>
Via the API, these can be accesses using the get_all_DBLinks method.<br>
<br>
For example, to get the hgnc symbol of a gene object, you could do
the following:<br>
<blockquote>my $hgnc_xrefs = $gene->get_all_DBLinks('HGNC');<br>
foreach my $xref (@$hgnc_xrefs) {<br>
print $xref->display_id . "\n";<br>
}<br>
<br>
</blockquote>
The same would work for RefSeq mRNAs<br>
<blockquote>my $refseq_xrefs =
$gene->get_all_DBLinks('Refseq_mRNA');<br>
foreach my $xref (@$refseq_xrefs) {<br>
print $xref->display_id . "\n";<br>
}<br>
</blockquote>
<br>
On a side note, in your script you set a logic_name
'refseq_human_import'.<br>
If you want to restrict your study to that specific logic_name, you
can specify it when fetching genes<br>
<blockquote>my $genes = $slice->get_all_Genes($logic_name);<br>
</blockquote>
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.<br>
Hence, you would need to change your adaptor call<br>
<blockquote>my $slice_adaptor = $registry->get_adaptor('Human',
'otherfeatures', 'Slice');<br>
</blockquote>
<br>
Hope that helps.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 25/06/13 13:12, Manam, Monica
(NIH/NCI) [F] wrote:<br>
</div>
<blockquote
cite="mid:11DC039F3170B8418685189040BEEF7027F2B7@MLBXV10.nih.gov"
type="cite">
<pre wrap="">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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</pre>
</blockquote>
<br>
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