<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks Will.<div><br></div><div>I love the plugin capability. I had been dreading moving my much-patched VEP 2.1 to each new version. Having made the one-time, non-trivial move to plugins, I am very happy with the decoupling and the performance.</div><div><br></div><div>Regarding my issue #1 (re input line), I had a problem with regulatory and motif features. This seems to work</div><div><br></div><div><div>my $input_line;</div><div>if ($tva->isa('Bio::EnsEMBL::Variation::TranscriptVariationAllele')){</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>$input_line = $tva->transcript_variation->base_variation_feature->{_line};</div><div>}</div><div>elsif($tva->isa('Bio::EnsEMBL::Variation::RegulatoryFeatureVariationAllele')){</div><div> $input_line = $tva->regulatory_feature_variation->base_variation_feature->{_line};</div><div>}</div><div>elsif($tva->isa('Bio::EnsEMBL::Variation::MotifFeatureVariationAllele')){</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>$input_line = $tva->motif_feature_variation->base_variation_feature->{_line};</div><div>}</div></div><div><br></div><div><div apple-content-edited="true">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-family: Helvetica; font-size: 12px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: 10px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><p class="MsoNormal"><font class="Apple-style-span" face="'Devanagari MT'" size="7"><span class="Apple-style-span" style="font-size: 27px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br class="Apple-interchange-newline"></span></font><font class="Apple-style-span" size="5"><span class="Apple-style-span" style="font-size: 18px; ">ॐ</span></font></span></font></p></span><p></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; line-height: 19px; font: normal normal normal 16px/normal Helvetica; "><span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: 10px; ">Michael Yourshaw</span></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">UCLA Geffen School of Medicine</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Department of Human Genetics, Nelson Lab</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">695 Charles E Young Drive S</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Gonda 5554</span></div><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Los Angeles CA 90095-8348 USA</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; color: rgb(0, 0, 153); "><span style="text-decoration: underline; letter-spacing: 0px; "><a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a></span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">970.691.8299</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 9px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately. Thank you.</span></p><div><font class="Apple-style-span" size="1"><span class="Apple-style-span" style="font-size: 9px; "><br></span></font></div></span><br class="Apple-interchange-newline"><br class="Apple-interchange-newline"></span></div>
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<br><div><div>On Jan 17, 2012, at 01:38, Will McLaren wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Michael,<br><br>Thanks for these tips - I hope you and others are finding the plugin<br>system useful!<br><br>Just a couple of comments:<br><br>On 17 January 2012 01:20, Michael Yourshaw <<a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a>> wrote:<br><blockquote type="cite">Here are a few suggestions that would be useful for VEP plugin developers.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">1. Make the original input line available to plugins. I do this by<br></blockquote><blockquote type="cite">patching VEP.pm, sub init_line, after "my $line = …", to add:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> $line->{_input_line} = $vf->{_line};<br></blockquote><br><br>There's actually no need to edit VEP.pm to access this - you can get<br>to the variation feature object through the object hierarchy of the<br>$tva TranscriptVariationAllele object that the plugin's run() method<br>receives:<br><br>my $input_line = $tva->transcript_variation->variation_feature->{_line};<br><br><blockquote type="cite"><br></blockquote><blockquote type="cite">2. Provide a way to preserve columns with a value of zero instead of<br></blockquote><blockquote type="cite">converting to ‘-‘. I do this in variant_effect_predictor.pl , sub<br></blockquote><blockquote type="cite">print_line, by changing:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> #$output = join "\t", map { $line->{$_} || '-' } @OUTPUT_COLS;<br></blockquote><blockquote type="cite"> $output = join "\t", map { $line->{$_} } @OUTPUT_COLS;<br></blockquote><br>This is a bug - it should probably be checking whether a column is<br>defined rather than whether it is non-zero. I'll fix this for the next<br>release.<br><br><blockquote type="cite"><br></blockquote><blockquote type="cite">3. Provide a way for plugins to see intergenic variants (when there is no<br></blockquote><blockquote type="cite">regulatory or transcript variation). It looks like the solution to this one<br></blockquote><blockquote type="cite">is a bit more complex, and may interact with my earlier post about problems<br></blockquote><blockquote type="cite">with not fully qualified feature types.<br></blockquote><br>Yes, this is a bit more tricky - we'll look into doing this for the<br>next release too. A couple of solutions come to mind, but none are<br>ideal.<br><br>Thanks again for the feedback<br><br>Will<br><br><blockquote type="cite"><br></blockquote><blockquote type="cite">ॐ<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Michael Yourshaw<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">UCLA Geffen School of Medicine<br></blockquote><blockquote type="cite">Department of Human Genetics, Nelson Lab<br></blockquote><blockquote type="cite">695 Charles E Young Drive S<br></blockquote><blockquote type="cite">Gonda 5554<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Los Angeles CA 90095-8348 USA<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">970.691.8299<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">This message is intended only for the use of the addressee and may contain<br></blockquote><blockquote type="cite">information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY<br></blockquote><blockquote type="cite">WORK PRODUCT. If you are not the intended recipient, you are hereby notified<br></blockquote><blockquote type="cite">that any dissemination of this communication is strictly prohibited. If you<br></blockquote><blockquote type="cite">have received this communication in error, please erase all copies of the<br></blockquote><blockquote type="cite">message and its attachments and notify us immediately. Thank you.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br></blockquote><blockquote type="cite">List admin (including subscribe/unsubscribe):<br></blockquote><blockquote type="cite"><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br></blockquote><blockquote type="cite">Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote><blockquote type="cite"><br></blockquote></div></blockquote></div><br></div></body></html>