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<p class="MsoNormal">Hi,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">STAR consortium’s website is down, and I have to download a bit of their genotyped SNPs to my system. However, the following code yielded no SNPs at all:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">my $rat_slice_adaptor=$registry->get_adaptor('rat','core','Slice');</p>
<p class="MsoNormal">my $var_fea_adaptor=$registry->get_adaptor('rat','variation','variationfeature');</p>
<p class="MsoNormal">my $pop_adaptor=$registry->get_adaptor('rat','variation','population');</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">my $rat_17=$rat_slice_adaptor->fetch_by_region('chromosome','17');</p>
<p class="MsoNormal">my $pop_code=$pop_adaptor->fetch_by_name('STAR:mdc/cng'); </p>
<p class="MsoNormal">my @rat_17_star_gtype;</p>
<p class="MsoNormal">if ($pop_code){@rat_17_star_gtype=@{$var_fea_adaptor->fetch_all_by_Slice_Population($rat_17,$pop_code)}};</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">print “No of SNPs: “,scalar(@rat_17_star_gtype);</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">The only other way I can think of to get this dataset is the following highly inefficient code:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">my $rat_slice_adaptor=$registry->get_adaptor('rat','core','Slice');</p>
<p class="MsoNormal">my $var_fea_adaptor=$registry->get_adaptor('rat','variation','variationfeature');</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">my $rat_17=$rat_slice_adaptor->fetch_by_region('chromosome','17');</p>
<p class="MsoNormal">my @genotyped_vars=@{$var_fea_adaptor->fetch_all_genotyped_by_Slice($rat_17)};</p>
<p class="MsoNormal">my @rat_17_star_gtype;</p>
<p class="MsoNormal">foreach $single_var(@genotyped_vars){</p>
<p class="MsoNormal">my @sources=@{$single_var->get_all_sources()};</p>
<p class="MsoNormal">foreach my $source (@sources){</p>
<p class="MsoNormal">if ($source eq ‘ENSEMBL:STAR/gtype’){</p>
<p class="MsoNormal">push (@rat_17_star_gtype, $single_var );</p>
<p class="MsoNormal">last;}</p>
<p class="MsoNormal">}</p>
<p class="MsoNormal">}</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Are there a slightly more efficient way to do this?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Cheers,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">John MC Ma</p>
<p class="MsoNormal">Graduate Assistant</p>
<p class="MsoNormal">Department of Pharmacology</p>
<p class="MsoNormal">The University of Iowa</p>
<p class="MsoNormal">Iowa City, IA, USA</p>
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