<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi,</div><div>You can use the AlignSlice to get the alignment, i.e. add the following lines:</div><div><br></div><div><div>my $align_slice_adaptor =</div><div> Bio::EnsEMBL::Registry->get_adaptor("Multi", "compara", "AlignSlice");</div></div><div><br></div><div><div><div>my $align_slice = $align_slice_adaptor->fetch_by_Slice_MethodLinkSpeciesSet($source_org_slice, $methodLinkSpeciesSet, 'expanded', 'restrict');</div><div><br></div><div>print $alignIO $align_slice->get_SimpleAlign;</div></div></div><div><br></div><div>I also used the "clustalw" as the format for AlignIO.</div><div><br></div><div>I hope that helps,</div><div>Cheers</div><div>Kathryn</div><br><div apple-content-edited="true">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Kathryn Beal, PhD<br>European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Trust Genome Campus, Hinxton<br>Cambridge CB10 1SD, UK <br>Tel. +44 (0)1223 494458<br><a href="http://www.ensembl.org/">www.ensembl.org</a><br></div></div></div>
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<br><div><div>On 28 Jan 2013, at 10:27, Eduardo Andrés León wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear all,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I'm trying to match the mouse sequence(2-28403186:28403879) into the human genome using ensembl 67.</div><div><br></div><div>Using the web, I've got the following :</div><div><br></div><div><a href="http://may2012.archive.ensembl.org/Mus_musculus/Location/Compara_Alignments?align=410&db=core&r=2%3A28403186-28403879">http://may2012.archive.ensembl.org/Mus_musculus/Location/Compara_Alignments?align=410&db=core&r=2%3A28403186-28403879</a></div><div><br></div><div><table style="color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); position: static; z-index: auto; "><tbody><tr style="vertical-align: top; "><th style="font-size: 1em; text-align: left; border: 0px; color: rgb(51, 51, 51); ">mus_musculus:2 > </th><td style="font-size: 1em; text-align: left; border: 0px; color: rgb(51, 51, 51); "><a href="http://may2012.archive.ensembl.org/Mus_musculus/Location/View?db=core;r=2:28403186-28403879" style="color: rgb(0, 0, 102); ">chromosome:NCBIM37:2:28403186:28403879:1</a><br></td></tr><tr style="vertical-align: top; "><th style="font-size: 1em; text-align: left; border: 0px; color: rgb(51, 51, 51); ">homo_sapiens:9 > </th><td style="font-size: 1em; text-align: left; border: 0px; color: rgb(51, 51, 51); "><a href="http://may2012.archive.ensembl.org/Homo_sapiens/Location/View?r=9:100149814-100149843" style="color: rgb(0, 0, 102); ">chromosome:GRCh37:9:100149814:100149843:-1</a><br><a href="http://may2012.archive.ensembl.org/Homo_sapiens/Location/View?r=GL000220.1:11378-11383" style="color: rgb(0, 0, 102); ">supercontig:GRCh37:GL000220.1:11378:11383:-1</a><br><a href="http://may2012.archive.ensembl.org/Homo_sapiens/Location/View?r=9:135978315-135979072" style="color: rgb(0, 0, 102); ">chromosome:GRCh37:9:135978315:135979072:-1</a><br><br></td></tr></tbody></table><br></div><div><br></div><div>But when I use the API, I obtain more than 55 fragments (attached as a zip file) :</div><div><br></div><div></div></div><span><alignment.3012.17691580863.txt.zip></span><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div 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></div>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></div><br></body></html>