<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Will—<div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class=""> 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 class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div dir="ltr" class=""><div class=""><div class=""> $output = join "\t", map {</div><div class=""> (defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ? $extra{$_} : $config->{empty_field_char}))</div><div class=""> } @{$config->{fields}};</div></div></div></blockquote><div class=""><div dir="ltr" class=""><div class=""><div class=""><br class=""></div><div class="">and allow -- empty_field_char with no argument to yield ‘’.</div></div></div></div><div apple-content-edited="true" class="">
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<br class=""><div><blockquote type="cite" class=""><div class="">On 3Dec, 2014, at 08:23, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" class="">wm2@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi G,<div class=""><br class=""></div><div class="">The print_line() subroutine in <a href="http://variant_effect_predictor.pl/" class="">variant_effect_predictor.pl</a> has the following code:</div><div class=""><br class=""></div><div class=""><div class=""> $output = join "\t", map {</div><div class=""> (defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ? $extra{$_} : '-'))</div><div class=""> } @{$config->{fields}};</div></div><div class=""><br class=""></div><div class="">So to do as you intend you could change this to</div><div class=""><br class=""></div><div class=""><div class=""> $output = join "\t", map {</div><div class=""> (defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ? $extra{$_} : ''))</div><div class=""> } @{$config->{fields}};</div></div><div class=""><br class=""></div><div class="">Regards</div><div class=""><br class=""></div><div class="">Will McLaren</div><div class="">Ensembl Variation</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On 3 December 2014 at 16:17, Genomeo Dev <span dir="ltr" class=""><<a href="mailto:genomeodev@gmail.com" target="_blank" class="">genomeodev@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi,<div class=""><br class=""></div><div class="">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 class="HOEnZb"><font color="#888888" class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class=""><div dir="ltr" class="">G.</div></div>
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