<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div></div><div><br></div><div>The code for extracting the data is the following :</div><div><br></div><div><div>getAlignMent(2,28403186,28403879);</div></div><div><br></div><div><div><span class="Apple-tab-span" style="white-space:pre"> </span>sub getAlignMent{</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my ($source_org_chr,$source_org_start,$source_org_end)=@_;</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>#Auto-configure the registry</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Bio::EnsEMBL::Registry->load_registry_from_db(</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>-host=>"<a href="http://ensembldb.cnio.es">ensembldb.cnio.es</a>",</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>-user=>"ensembl");</div><div><br></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span># Get the Compara Adaptor for MethodLinkSpeciesSets</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my $method_link_species_set_adaptor =</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> Bio::EnsEMBL::Registry->get_adaptor(</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> "Multi", "compara", "MethodLinkSpeciesSet");</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span># Get the MethodLinkSpecieSet for source_org-mouse lastz-net alignments</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my $methodLinkSpeciesSet = $method_link_species_set_adaptor-></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>fetch_by_method_link_type_registry_aliases("BLASTZ_NET", ["mouse", "human"]);</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span># Define the start and end positions for the alignment</div><div><span class="Apple-tab-span" style="white-space:pre"> </span># Get the source_org *core* Adaptor for Slices</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my $source_org_slice_adaptor =</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> Bio::EnsEMBL::Registry->get_adaptor(</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> "mouse", "core", "Slice");</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span># Get the slice corresponding to the region of interest</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my $source_org_slice = $source_org_slice_adaptor->fetch_by_region(</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> "chromosome", $source_org_chr, $source_org_start, $source_org_end);</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span># Get the Compara Adaptor for GenomicAlignBlocks</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my $genomic_align_block_adaptor =</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> Bio::EnsEMBL::Registry->get_adaptor(</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> "Multi", "compara", "GenomicAlignBlock");</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span># The fetch_all_by_MethodLinkSpeciesSet_Slice() returns a ref.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span># to an array of GenomicAlingBlock objects (source_org is the reference species) </div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my $all_genomic_align_blocks = $genomic_align_block_adaptor-></div><div><span class="Apple-tab-span" style="white-space:pre"> </span> fetch_all_by_MethodLinkSpeciesSet_Slice(</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> $methodLinkSpeciesSet, $source_org_slice, undef, undef, "restrict");</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span># set up an AlignIO to format SimpleAlign output</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my $outputAl="alignment." . rand(10000) . ".txt";</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>open(OUT,">$outputAl") || die "3 $!\n";</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>my $alignIO = Bio::AlignIO->newFh(-interleaved => 0,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> -fh => \*OUT,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> -format => 'pfam',</div><div><span class="Apple-tab-span" style="white-space:pre"> </span> -idlength => 20);</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span># print the restricted alignments</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>if (scalar(@{$all_genomic_align_blocks})==0){</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>open(NMR,">>chr$source_org_chr\_No_mapping_regions.txt") || die "$!\n";</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>print NMR "$source_org_chr\t$source_org_start\t$source_org_end\n";</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>close NMR;</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>return();</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>}</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>else{</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>foreach my $genomic_align_block ( @{ $all_genomic_align_blocks } ) {</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>print $alignIO $genomic_align_block->get_SimpleAlign;</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>}</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>close OUT;</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>}</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>}</div></div><div><br></div><div>This same happens with other segments, but not all of them.</div><div><br></div><div>So, can anybody tell me how to extract the same records the web shows ?</div><div><br></div><div>Regards and thanks in advance !</div><div><br></div><div><br></div><div><br></div><div><br></div></body></html>