<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr" class="gmail_signature"><div>Dear Developers </div><div><br></div><div>I created a simple script to provide me with polymorphic frequencies in the different populations in the database. However after running it on my set it seems some variations do not show results</div><div><br></div><div><br></div>take for example the INDEL rs141080692 <div> </div><div>When I run it though my script this is the information I get:</div><div><br></div><div><div>rs141080692     GT      1000GENOMES:pilot_1_CEU_low_coverage_panel      -       deletion        9       123543905       123543907</div><div>rs141080692     -       1000GENOMES:pilot_1_CEU_low_coverage_panel      -       deletion        9       123543905       123543907</div><div>rs141080692     GT      1000GENOMES:pilot_1_CHB+JPT_low_coverage_panel  -       deletion        9       123543905       123543907</div><div>rs141080692     -       1000GENOMES:pilot_1_CHB+JPT_low_coverage_panel  -       deletion        9       123543905       123543907</div><div>rs141080692     GT      1000GENOMES:pilot_1_YRI_low_coverage_panel      -       deletion        9       123543905       123543907</div><div>rs141080692     -       1000GENOMES:pilot_1_YRI_low_coverage_panel      -       deletion        9       123543905       123543907</div><div>rs141080692     GT      GMI:AK_Koreans  -       deletion        9       123543905       123543907</div><div>rs141080692     -       GMI:AK_Koreans  -       deletion        9       123543905       123543907</div><div>rs141080692     GT      GMI:NA10851     -       deletion        9       123543905       123543907</div><div>rs141080692     -       GMI:NA10851     -       deletion        9       123543905       123543907</div><div>rs141080692     GT      SSMP:SSM        -       deletion        9       123543905       123543907</div><div>rs141080692     -       SSMP:SSM        -       deletion        9       123543905       123543907</div></div><div><br></div><div>however, looking at the same database in your website:</div><div><br></div><div><a href="http://dec2015.archive.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=9:123543406-123544407;v=rs141080692;vdb=variation;vf=127601209">http://dec2015.archive.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=9:123543406-123544407;v=rs141080692;vdb=variation;vf=127601209</a><br></div><div><br></div><div>You can see that there is information about its frequency in a whole bunch of populations</div><div><br></div><div>How do I go about fetching these?</div><div><br></div><div>My script is pretty basic</div><div><br></div><div>first I fect all populations or only ones I am interested in with:</div><div><br></div><div><div>foreach my $pop (@{$population_adaptor->fetch_all()}){</div><div><span style="white-space:pre">   </span>my $name = $pop->name();</div><div><span style="white-space:pre">   </span>if (defined $name){</div><div><span style="white-space:pre">           </span>if (defined $population){</div><div><span style="white-space:pre">                     </span>if ($name =~ /\Q$population/){</div><div><span style="white-space:pre">                                </span>print STDERR "Selected Populations: $name \n";</div><div><span style="white-space:pre">                              </span>push @selected_populations, $name; </div><div><span style="white-space:pre">                  </span>}</div><div><span style="white-space:pre">             </span>}else{</div><div><span style="white-space:pre">                        </span>print STDERR "Selected Populations: $name \n";</div><div><span style="white-space:pre">                      </span>push @selected_populations, $name; </div><div><span style="white-space:pre">                  </span></div><div><span style="white-space:pre">              </span>}</div><div><span style="white-space:pre">     </span>}</div><div>}</div></div><div><br></div><div>I then use the variation adaptor to get the variation object</div><div><br></div><div><div> my $variation = $variation_adaptor->fetch_by_name($id);</div></div><div><br></div><div>Then I cycle though each variation feature with </div><div><br></div><div><div>foreach my $vf (@{$vf_adaptor->fetch_all_by_Variation($var)}){</div></div><div><div><span style="white-space:pre">              </span>my @alleles = @{$vf->get_all_Alleles};</div></div><div><br></div><div><div><span style="white-space:pre">             </span>ALLELE_CYCLE:foreach my $a (@alleles){</div><div><span style="white-space:pre">                        </span>my $astr = $a->allele();</div><div><span style="white-space:pre">                   </span>my $pop  = $a->population();</div><div><span style="white-space:pre">                      </span>my $pop_name = "-";</div><div><span style="white-space:pre">                 </span>if (defined $pop){</div><div><span style="white-space:pre">                            </span>$pop_name = $a->population->name() ;</div><div><span style="white-space:pre">                    </span>}</div><div><span style="white-space:pre">                     </span>my $freq = $a->frequency() || "-";</div><div><span style="white-space:pre">                       </span></div><div><span style="white-space:pre">                      </span>foreach my $p (@{$selected_populations}){</div><div><span style="white-space:pre">                             </span>#print STDERR $pop_name."\t".$p."\n";</div><div><span style="white-space:pre">                             </span>if ($pop_name eq $p){</div><div><span style="white-space:pre">                                 </span>print $out_fh join "\t", (<span style="white-space:pre"> </span>$var->name(),</div><div><span style="white-space:pre">                                                                                              </span>$astr,</div><div><span style="white-space:pre">                                                                                                </span>$pop_name,</div><div><span style="white-space:pre">                                                                                            </span>$freq,</div><div><span style="white-space:pre">                                                                                                </span>$varClass, </div><div><span style="white-space:pre">                                                                                          </span>$chr, </div><div><span style="white-space:pre">                                                                                               </span>$start, </div><div><span style="white-space:pre">                                                                                             </span>$end."\n");</div><div><span style="white-space:pre">                                 </span>next ALLELE_CYCLE;</div><div><span style="white-space:pre">                            </span>}</div><div><span style="white-space:pre">                     </span>}</div><div><span style="white-space:pre">             </span>}</div></div><div>}</div><div><br></div><div>Am I doing something wrong? </div><div>There are the phase3 population data for example. They are clealy included in your site</div><div><br></div><div>Many thanks</div><div><br></div><div>Duarte</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div></div></div></div></div></div></div></div></div></div>