[ensembl-dev] empty values in variant_effect_predictor.pl

[Michael Yourshaw]

Hi Will—

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.

 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

>         $output = join "\t", map {
>             (defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ? $extra{$_} : $config->{empty_field_char}))
>         } @{$config->{fields}};

and allow -- empty_field_char with no argument to yield ‘’.

ॐ

Michael Yourshaw, PhD
UCLA Geffen School of Medicine
Department of Pediatrics
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu <mailto:myourshaw at ucla.edu>
970.691.8299

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> On 3Dec, 2014, at 08:23, Will McLaren <wm2 at ebi.ac.uk> wrote:
> 
> Hi G,
> 
> The print_line() subroutine in variant_effect_predictor.pl <http://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 <mailto: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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