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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>cheers monika<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>serves me right for blithely cut and pasting…<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Do you think that the best way to get patched genes is : <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>my @genes = @{ $gene_adaptor->fetch_all_by_display_label($gene->display_xref()->display_id()) };</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>or is there another way?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>trevor<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span style='font-family:"Arial","sans-serif";color:navy'>Trevor Paterson PhD<br></span></b><span style='font-family:"Arial","sans-serif";color:navy'><a href="mailto:trevor.paterson@roslin.ed.ac.uk">trevor.paterson@roslin.ed.ac.uk</a></span><span style='color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Arial","sans-serif";color:navy'>Bioinformatics <br>The Roslin Institute<br>Royal (Dick) School of Veterinary Studies<br>University of Edinburgh<br>Easter Bush<br>Midlothian<br>EH25 9RG<br>Scotland UK<br><br>phone +44 (0)131 651 9157<br><br><a href="http://bioinformatics.roslin.ed.ac.uk/">http://bioinformatics.roslin.ed.ac.uk/</a></span><span style='color:black'><br></span><span style='font-size:10.0pt;color:navy'><br></span><span style='font-family:"Arial","sans-serif";color:green'>Please consider the environment before printing this e-mail</span><span style='color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><i><span style='font-size:10.0pt;color:navy'>The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336</span></i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'><br><b>Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.</b></span><span style='color:#1F497D'> <o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Monika Komorowska [mailto:monika@ebi.ac.uk] <br><b>Sent:</b> 25 June 2012 14:03<br><b>To:</b> PATERSON Trevor<br><b>Cc:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] Wrongly documented gene_adaptor method ?<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Trevor<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Apologies, but we seem to have the wrong method called in the example for fetch_all_by_display_label<o:p></o:p></p></div><div><p class=MsoNormal>It should state: <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Example : my @genes = @{$geneAdaptor->fetch_all_by_display_label("PPP1R2P1")};<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I committed the change to the GeneAdaptor 'fetch_all_by_display_label' method documentation head code, which will be released in a month with release 68.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>fetch_all_by_display_label (as Bert mentioned) will return an arrayref of genes.<o:p></o:p></p></div><div><p class=MsoNormal>Sorry about the confusion which the wrong example has caused.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thanks<o:p></o:p></p></div><div><p class=MsoNormal>Monika<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On 25 Jun 2012, at 13:50, PATERSON Trevor wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>According to the Perl documentation, you should be able to get a list of genes for a given display label, using:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>public Listref Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_all_by_display_label ( )<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>However, this method is wrongly documented in the online perl docs, and does not return an array – but a single gene object<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><pre><span style='color:black'>my @genes = @{$geneAdaptor->fetch_by_display_label(<span class=stringliteral>"</span></span><span style='font-family:Consolas;color:black'>TBC1D3B</span><span class=stringliteral><span style='color:black'>"</span></span><span style='color:black'>)};</span><o:p></o:p></pre><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>DEBUGGER ERROR MESSAGE : Not an ARRAY reference</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:red'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>When you look at the real code in Release 67 API, rather than the www perldocs, the method actually returns a single gene, preferring one that is on a reference slice.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:red'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>I am looking for a way of getting alternative gene models on Patch exceptions: and this method would have been promising. e.g for the gene<span class=apple-converted-space> </span></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><a href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224226;r=HG75_PATCH:34442621-34976908"><span style='color:black'>ENSG00000224226</span></a><span class=apple-converted-space> </span>Location<span class=apple-converted-space> </span><a href="http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000224226;r=17:34493061-34503984"><span style='color:black'>Chromosome 17: 34,493,061-34,503,984</span></a></span><span class=apple-converted-space><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span></span><span style='font-size:10.0pt;font-family:Consolas;color:black'>how do I get its equivalent on the patch-fix<span class=apple-converted-space> </span></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><a href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260069;r=HG75_PATCH:34442621-34976908"><span style='color:black'>ENSG00000260069</span></a><span class=apple-converted-space> </span>Location<span class=apple-converted-space> </span><a href="http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000260069;r=HG75_PATCH:34493132-34503984"><span style='color:black'>Chromosome HG75_PATCH: 34,493,132-34,503,984</span></a>.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>obviously I can dig into the API and call the appropriate sql code myself:</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>my $constraint = "x.display_label = '". $gene->display_xref()->display_id()."' AND g.is_current = 1";</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>my @same_labelled_genes = @{ $gene_adaptor->generic_fetch($constraint) };</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>but is there an alternative (simple) method to get either ‘same_labelled’ genes or ideally ‘equivalent-exception’ genes for a given gene?</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>the method</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>public Listref Bio::EnsEMBL::Gene::get_all_alt_alleles ( )<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>of course does something similar using the alt_alleles table , but only for alternative haplotypes not patches.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>Thanks</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>Trevor</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:#B22200'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:#B22200'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><b><span style='font-family:"Arial","sans-serif";color:navy'>Trevor Paterson PhD<br></span></b><span style='font-family:"Arial","sans-serif";color:navy'><a href="mailto:trevor.paterson@roslin.ed.ac.uk">trevor.paterson@roslin.ed.ac.uk</a></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:navy'>Bioinformatics<span class=apple-converted-space> </span><br>The Roslin Institute<br>Royal (Dick) School of Veterinary Studies<br>University of Edinburgh<br>Easter Bush<br>Midlothian<br>EH25 9RG<br>Scotland UK<br><br>phone +44 (0)131 651 9157<br><br><a href="http://bioinformatics.roslin.ed.ac.uk/">http://bioinformatics.roslin.ed.ac.uk/</a></span><span style='color:black'><br></span><span style='font-size:10.0pt;color:navy'><br></span><span style='font-family:"Arial","sans-serif";color:green'>Please consider the environment before printing this e-mail</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-size:10.0pt;color:navy'>The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336</span></i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'><br><b>Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.</b></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif"'>The University of Edinburgh is a charitable body, registered in<br>Scotland, with registration number SC005336.<br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe):<span class=apple-converted-space> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog:<span class=apple-converted-space> </span><a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><div><div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black'>Monika Komorowska<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black'>EnsEMBL Software Developer<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black'>European Bioinformatics Institute (EMBL-EBI)<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black'>tel: +44(0) 1233 494 409<o:p></o:p></span></p></div></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>