<div dir="ltr">Thanks Michael, I've updated the plugin.<div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 14 November 2013 21:35, Michael Yourshaw <span dir="ltr"><<a href="mailto:myourshaw@ucla.edu" target="_blank">myourshaw@ucla.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">I’m not sure this is the right list to bring this up, but the dbNSFP plugin can cause a problem on non-windows machines.<div>
<br></div><div>The symptom is that if you select the <span style="font-size:12px">ESP6500_EA_AF column option for this plugin, the Extra column in the VEP output will have a CR that might be interpreted as a line break immediately after the ESP6500_EA_AF value</span><span style="font-size:12px">.</span></div>
<div><span style="font-size:12px"><br></span></div><div><span style="font-size:12px">This is because the </span>dbNSFP data file has windows-style (CRLF) newlines and <span style="font-size:12px">ESP6500_EA_AF is the last column in each record.</span></div>
<div><span style="font-size:12px"><br></span></div><div><span style="font-size:12px">An easy fix is to add a cleanup line in the </span>dbNSFP plugin:</div><div><div> while(<TABIX>) {</div></div><div><div><span style="white-space:pre-wrap"> </span>chomp;</div>
<div><span style="white-space:pre-wrap"> </span>#remove trailing CR on linux platforms</div><div><span style="white-space:pre-wrap"> </span>s/\r$//g;</div><div><span style="white-space:pre-wrap"> </span>my @split = split /\t/;</div>
</div><div><br></div><div>You might consider having VEP recode any forbidden semicolon, tab, CR, or LF (or other?) values that any plugin adds to EXTRA.</div><div><div>
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</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 style="font-family:'Lucida Grande';font-size:10px">Michael Yourshaw</span></p>
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<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'">
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