[ensembl-dev] empty values in variant_effect_predictor.pl

Will McLaren wm2 at ebi.ac.uk
Wed Dec 3 16:23:36 GMT 2014


Hi G,

The print_line() subroutine in variant_effect_predictor.pl has the
following code:

        $output = join "\t", map {
            (defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ?
$extra{$_} : '-'))
        } @{$config->{fields}};

So to do as you intend you could change this to

        $output = join "\t", map {
            (defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ?
$extra{$_} : ''))
        } @{$config->{fields}};

Regards

Will McLaren
Ensembl Variation

On 3 December 2014 at 16:17, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi,
>
> 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.
>
> --
> G.
>
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