<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Hardip,<div><br></div><div>At a glance your code looks fine. I'm not sure why it is slow. Are you connecting to our MySQL (host <a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a> port 5306) or do you have local copies of the databases?</div><div><br></div><div>If you are only interested in one biotype eg. protein-coding then you could modify your gene-fetch query like:</div><div><span class="Apple-style-span" style="font-family: Calibri, Verdana, Helvetica, Arial; font-size: 15px; ">foreach my $gene (@{$slice->get_all_Genes(undef, undef, undef, undef, 'protein_coding')}){</span></div><div><br></div><div>Cheers,</div><div>Bronwen</div><div><br></div><div><br><div><div>On 11 Oct 2010, at 06:06, Hardip Patel wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>
<font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt">Dear all<br>
<br>
I am trying to fetch gene centred information using following code. It takes a long time to extract information for all genes from human or mice at least.<br>
<br>
I was wondering if the following code could be optimized to get information faster.<br>
<br>
my $slice_adaptor = $registry->get_adaptor($spec, 'Core', 'slice');<br>
foreach my $slice (@{$slice_adaptor->fetch_all('toplevel')}){<br>
foreach my $gene (@{$slice->get_all_Genes}){<br>
foreach my $transcript (@{$gene->get_all_Transcripts}){<br>
foreach my $exon (@{$transcript->get_all_Exons}){<br>
####get transcript, UTR, exon, and intron start and end in cDNA coordinates and genomic coordinates<br>
}<br>
}<br>
}<br>
}<br>
------<br>
<br>
Regards<br>
<br>
-- <br>
</span><span style="font-size:12pt">Hardip R. Patel<br>
</span><span style="font-size:11pt"><br>
VCCRI 12th International Symposium <br>
<font color="#008FFE">“Charting the depths of RNA: from molecules to therapies”<br>
</font>19 November 2010<br>
visit <font color="#0000FF"><u><a href="http://www.victorchang.edu.au/">http://www.victorchang.edu.au</a></u></font> for details<br>
<br>
<br>
</span></font>
</div>
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