[ensembl-dev] empty values in variant_effect_predictor.pl

[Will McLaren]

The coordinates are formatted by format_coords() in VEP.pm; it should be
obvious what to change in there.

I'll look into doing as Michael suggests for 79; shame this discussion
didn't happen a few days ago as we released 78 yesterday!

Will

On 4 December 2014 at 11:42, Genomeo Dev <genomeodev at gmail.com> wrote:

> 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
>>
>> 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 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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