<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I don’t think that would work well as a general solution. What about implementing a specific hash key to designate text that would be output before the column info, such as “$$PRELUDE”? The value associated with the $$PRELUDE key would be put into the header before the column info. If the value were multiline (\n separated” VEP could nicely add the “##” before each line, so VEP maintains control over how the header is formatted.<div><br></div><div><br></div><div>This is obviously not a big deal, but would be a convenience.<br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; 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: 0; "><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; 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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; 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<br><div><div>On Apr 5, 2012, at 01:30, Graham Ritchie wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Michael,<br><br>One simple way to add arbitrary text to the header would be to just return the text you want to include as a key with the empty string as a value in the hash returned from the get_header_info method in your plugin, e.g.:<br><br>sub get_header_info {<br> return {<br> 'Human Protein Atlas expression profile data' => '',<br> 'HPA_ovary_follicle_cells' => "Expression profile for protein in human ovary follicle cells based on immunohistochemisty",<br><span class="Apple-tab-span" style="white-space:pre"> </span>'HPA_breast_glandular_cells' => "Expression profile for protein in human breast glandular cells based on immunohistochemisty",<br> };<br>}<br><br>Having a key in this hash does not require there to be a corresponding column. However, because the entries are returned in a hash, currently lines will be added to the header in an arbitrary order, so the code above will produce the header:<br><br>## HPA_breast_glandular_cells : Expression profile for protein in human breast glandular cells based on immunohistochemisty<br>## Human Protein Atlas expression profile data : <br>## HPA_ovary_follicle_cells : Expression profile for protein in human ovary follicle cells based on immunohistochemisty<br><br>It would be straightforward to sort the keys of this hash to fix the order, but then you'd have to include extra text to ensure this (e.g. prefixing each key with a number). Do you think this would be useful?<br><br>Cheers,<br><br>Graham<br><br><br>On 5 Apr 2012, at 09:02, Will McLaren wrote:<br><br><blockquote type="cite">Hi Michael,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Unfortunately no, the headers are added by the main VEP code before<br></blockquote><blockquote type="cite">any of the plugin-specific code is run.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">You could easily add this with a simple perl one liner or awk though?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Cheers<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Will<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 5 April 2012 02:27, Michael Yourshaw <<a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a>> wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite">Does VEP support a mechanism whereby a plugin can add ## comments to the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">output header without causing the creation of a column?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">For example, I might want the header to contain an introductory line,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">followed by two annotation column definitions:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">## Human Protein Atlas expression profile data:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">## HPA_ovary_follicle_cells : Expression profile for protein in human<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ovary follicle cells based on immunohistochemisty<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">## HPA_breast_glandular_cells : Expression profile for protein in human<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">breast glandular cells based on immunohistochemisty<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ॐ<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Michael Yourshaw<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">UCLA Geffen School of Medicine<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Department of Human Genetics, Nelson Lab<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">695 Charles E Young Drive S<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Gonda 5554<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Los Angeles CA 90095-8348 USA<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">970.691.8299<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">This message is intended only for the use of the addressee and may contain<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">WORK PRODUCT. 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