[ensembl-dev] empty values in variant_effect_predictor.pl

[Genomeo Dev]

When I tired that I noticed some of the fields such as cDNA_position,
CDS_position, Protein_position  as well as Extra still show the dash.

G.

On 3 December 2014 at 16:30, Genomeo Dev <genomeodev at gmail.com> wrote:

> Excellent thanks Will!
>
>
> On 3 December 2014 at 16:23, 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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>>
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>>
>
>
> --
> G.
>



-- 
G.
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