[ensembl-dev] VEP feature requests

[Will McLaren]

Hi Michael,

Thanks for these tips - I hope you and others are finding the plugin
system useful!

Just a couple of comments:

On 17 January 2012 01:20, Michael Yourshaw <myourshaw at ucla.edu> wrote:
> Here are a few suggestions that would be useful for VEP plugin developers.
>
> 1. Make the original input line available to plugins. I do this by
> patching VEP.pm, sub init_line, after "my $line = …", to add:
>
>     $line->{_input_line} = $vf->{_line};


There's actually no need to edit VEP.pm to access this - you can get
to the variation feature object through the object hierarchy of the
$tva TranscriptVariationAllele object that the plugin's run() method
receives:

my $input_line = $tva->transcript_variation->variation_feature->{_line};

>
> 2. Provide a way to preserve columns with a value of zero instead of
> converting to ‘-‘. I do this in variant_effect_predictor.pl , sub
> print_line,  by changing:
>
>        #$output = join "\t", map { $line->{$_} || '-' } @OUTPUT_COLS;
>         $output = join "\t", map { $line->{$_} } @OUTPUT_COLS;

This is a bug - it should probably be checking whether a column is
defined rather than whether it is non-zero. I'll fix this for the next
release.

>
> 3. Provide a way for plugins to see intergenic variants (when there is no
> regulatory or transcript variation). It looks like the solution to this one
> is a bit more complex, and may interact with my earlier post about problems
> with not fully qualified feature types.

Yes, this is a bit more tricky - we'll look into doing this for the
next release too. A couple of solutions come to mind, but none are
ideal.

Thanks again for the feedback

Will

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> ॐ
>
> Michael Yourshaw
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> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
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