<div dir="ltr">Thanks again Michael, fixed.<div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 14 November 2013 02:24, 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">Thanks for the quick response, Will.<div><br></div><div>Now there is a different issue. The quotes get passed through to the plugin.</div>
<div><br></div><div>For example, in FATHMM, the <span style="font-family:Monaco;font-size:10px">$self->{command}</span> is</div><div><br></div><div><div style="margin:0px;font-size:10px;font-family:Monaco"><span style="white-space:pre-wrap"> </span>"python /share/apps/myourshaw/VEP_plugins/fathmm/fathmm.py”</div>
<div style="margin:0px;font-size:10px;font-family:Monaco"><br></div><div style="margin:0px;font-size:10px;font-family:Monaco">rather than</div><div style="margin:0px;font-size:10px;font-family:Monaco"><br></div><div style="margin:0px">
<div style="font-family:Monaco;font-size:10px;margin:0px"><span style="white-space:pre-wrap"> </span>python /share/apps/myourshaw/VEP_plugins/fathmm/fathmm.py</div><div style="font-family:Monaco;font-size:10px;margin:0px">
<br></div><div style="font-family:Monaco;font-size:10px;margin:0px">The plugin throws an exception when it tries to run the command parameter (surrounded by quotes) in the shell in the line</div><div style="font-family:Monaco;font-size:10px;margin:0px">
<br></div><div style="font-family:Monaco;font-size:10px;margin:0px"><span style="white-space:pre-wrap"> </span>my $fathmm_err = `cd $command_dir; $command $tmp_in_file $tmp_out_file;`;</div><div style="font-family:Monaco;font-size:10px;margin:0px">
<br></div><div style="font-family:Monaco;font-size:10px;margin:0px">I think what’s needed in VEP is to change this line</div><div style="margin:0px"><div style="margin:0px"><font face="Monaco" size="1"> # remove quotes</font></div>
<div style="margin:0px"><font face="Monaco" size="1"> s/[\"\']//g;</font></div><div style="font-family:Monaco;font-size:10px">to</div><div><div><font face="Monaco" size="1"> # remove quotes</font></div>
<div><font face="Monaco" size="1"> s/[\"\']//g for @split;</font></div><div style="font-family:Monaco;font-size:10px"><br></div></div></div></div><div class="im"><div><span style="border-collapse:separate;font-size:12px;border-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:12px;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:12px;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:10px;white-space:normal;font-family:'Lucida Grande';word-spacing:0px"><p class="MsoNormal">
<font face="'Devanagari MT'" size="7"><span style="font-size:27px"><font size="5"><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 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>
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<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>
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<br></div><div><div class="h5"><div><div>On Nov 13, 2013, at 00:52, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:</div><br><blockquote type="cite"><div dir="ltr">Hi Michael,<div>
<br>Thanks for finding this; I've committed a fix to the CVS (branch 73).</div><div><br></div><div>It should work now if you use quotes - it won't work if you don't have quotes due to the way the config parser has to work.</div>
<div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 13 November 2013 02:43, 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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word">I’m having a problem with the FATHMM plugin parameters. I think this will affect all plugins that need a space in the text when the plugin is specified in a configuration file.<div>
<br></div><div>The plugin wants to be specified like this:</div><div>FATHMM,"python /path/to/fathmm/fathmm.py”</div><div><br></div><div>I am using a configuration file with parameters in that form, but the VEP read_config_from_file subroutine seems to be splitting on the space between ‘python’ and ‘/path/to’. This happens whether I use the enclosing double quotes or not.</div>
<div><br></div><div>The space in a plugin parameter isn’t a problem on the command line, just in a config file.</div><div><br></div><div><br><div>
<span style="border-collapse:separate;font-size:12px;border-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:12px;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:12px;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:10px;white-space:normal;font-family:'Lucida Grande';word-spacing:0px"><p class="MsoNormal">
<font face="'Devanagari MT'" size="7"><span style="font-size:27px"><font face="'Lucida Grande'" size="3"><span style="font-size:12px"><br></span></font><font size="5"><span style="font-size:18px">ॐ</span></font></span></font></p>
</span><div><br></div><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>
<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" target="_blank">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"><a href="tel:970.691.8299" value="+19706918299" target="_blank">970.691.8299</a></span></p><p style="margin-top:0px;margin-right:0px;margin-bottom:6px;margin-left:0px;font:normal normal normal 9px/normal 'Lucida Grande'">
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