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Dear all,
<div class="">I’m using an old script to obtain snp frequencies in different populations/subpolulations. I think it was made one year ago and obviously it is not working anymore. The think is that i made a few changes but I’m not able to update it correctly</div>
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<div class="">I hope any of you could help me.</div>
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<div class="">As an example, what I want is to obtain the frequency for the All population, EUR population and IBS sub-population (all from 1000 genomes):</div>
<div class=""><a href="http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=6:43769593-43770593;v=rs1570360;vdb=variation;vf=1121901" class="">http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=6:43769593-43770593;v=rs1570360;vdb=variation;vf=1121901</a></div>
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<div class="">My code was:</div>
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<div class="">my $variation = $variation_adaptor->fetch_by_name($snp);</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>if($variation){</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>foreach my $vf (@{$variation_adaptor_feature->fetch_all_by_Variation($variation)}) {</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>if($vf->seq_region_name !~ /^HG/){</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>print MAP $vf->seq_region_name() ." $snp 0 " .$vf->seq_region_start(),"\n";</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>print POB "$snp\t" . $vf->display_consequence;</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>foreach my $allele (@{$vf->get_all_Alleles}){</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>next unless (defined $allele->population);</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $allele_string = $allele->allele;</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $frequency = $allele->frequency || 'NA';</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $population_name = $allele->population->name;</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span> if($population_name eq "1000GENOMES:phase_1_IBS"){</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>print POB "\t$allele_string\t$frequency";</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span> }elsif($population_name eq "1000GENOMES:EUR"){</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>print POB "\t$allele_string\t$frequency";</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span> }elsif($population_name eq "1000GENOMES:phase_1_ALL"){</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>print POB "\t$allele_string\t$frequency”;</div>
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<div class="">.....</div>
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<div class="">So from the snp, I obtained the alleles and from the allele object I obtain most of the information using the population_name</div>
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<div class="">Now I have tried a couple of things without success</div>
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<div class=""><b class="">Example1:</b></div>
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<div class="">my $pa = $registry->get_adaptor("human","variation","population");</div>
<div class="">my $pop<span class="Apple-tab-span" style="white-space:pre"> </span>
= $allele->population;</div>
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<div class="">foreach my $super_pop (@{$pa->fetch_all_by_sub_Population($pop)}) {</div>
<div class=""> print $pop->name(), " is a super population of ", $super_pop->name(), "\n";</div>
<div class=""> }</div>
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<div class=""># fetch all sub populations of a population</div>
<div class=""> foreach my $sub_pop (@{$pa->fetch_all_by_super_Population($pop)}) {</div>
<div class=""> print $sub_pop->name(), " is a sub population of ", $pop->name(), "\n";</div>
<div class="">}</div>
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<div class=""><b class="">Example 2:</b></div>
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<div class="">my $pop<span class="Apple-tab-span" style="white-space: pre;"> </span>
= $allele->population;</div>
<div class="">my $sub_pops = $pop->get_all_sub_Populations();</div>
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<div class=""> foreach my $sp (@$sub_pops) {</div>
<div class=""> print </div>
<div class=""> 'name: ', $sp->name(),</div>
<div class=""> 'desc: ', $sp->description(),</div>
<div class=""> 'size: ', $sp->size(),"\n";</div>
<div class=""> }</div>
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<div class="">Any help ?</div>
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