<div dir="ltr">Personally, for now, since I am about to start running VEP, I will be happy Will if you could point me all the places where I can patch the code to get rid of the dashes.<div><br></div><div>G.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 3 December 2014 at 16:49, 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">Hi Will—<div><br></div><div>I suspect this is an issue for many others, as well. For one thing, in a database table the dash requires what should be a numerical field to be treated like text.</div><div><br></div><div> I deal with the dashes in post-processing, but as G says this can be a pain. Rather than users having to patch each new version of VEP, could you consider adding a new parameter so your code would look like</div><div><br></div><div><blockquote type="cite"><div dir="ltr"><div><span class=""><div> $output = join "\t", map {</div></span><div> (defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ? $extra{$_} : $config->{empty_field_char}))</div><div> } @{$config->{fields}};</div></div></div></blockquote><div><div dir="ltr"><div><div><br></div><div>and allow -- empty_field_char with no argument to yield ‘’.</div></div></div></div><div>
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<br><div><blockquote type="cite"><div>On 3Dec, 2014, at 08:23, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:</div><br><div><div dir="ltr">Hi G,<div><br></div><div>The print_line() subroutine in <a href="http://variant_effect_predictor.pl/" target="_blank">variant_effect_predictor.pl</a> has the following code:</div><div><br></div><div><div> $output = join "\t", map {</div><div> (defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ? $extra{$_} : '-'))</div><div> } @{$config->{fields}};</div></div><div><br></div><div>So to do as you intend you could change this to</div><div><br></div><div><div> $output = join "\t", map {</div><div> (defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ? $extra{$_} : ''))</div><div> } @{$config->{fields}};</div></div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 3 December 2014 at 16:17, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>Current VEP script puts dash in empty fields in the default output. Could you please point me to the code where I can remove replace dash with an empty string? Modifying the output file after it is generated is non-trivial for very large files.<span><font color="#888888"><br clear="all"><div><br></div>-- <br><div><div dir="ltr">G.</div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr">G.</div></div>
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