[ensembl-dev] empty values in variant_effect_predictor.pl

[Genomeo Dev]

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.

G.

On 3 December 2014 at 16:49, Michael Yourshaw <myourshaw at ucla.edu> wrote:

> 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
>
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>
> myourshaw at ucla.edu
>
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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 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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-- 
G.
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