[ensembl-dev] VEP feature requests

[Michael Yourshaw]

Thanks Will.

I love the plugin capability. I had been dreading moving my much-patched VEP 2.1 to each new version. Having made the one-time, non-trivial move to plugins, I am very happy with the decoupling and the performance.

Regarding my issue #1 (re input line), I had a problem with regulatory and motif features. This seems to work

my $input_line;
if ($tva->isa('Bio::EnsEMBL::Variation::TranscriptVariationAllele')){
	$input_line = $tva->transcript_variation->base_variation_feature->{_line};
}
elsif($tva->isa('Bio::EnsEMBL::Variation::RegulatoryFeatureVariationAllele')){
    $input_line = $tva->regulatory_feature_variation->base_variation_feature->{_line};
}
elsif($tva->isa('Bio::EnsEMBL::Variation::MotifFeatureVariationAllele')){
	$input_line = $tva->motif_feature_variation->base_variation_feature->{_line};
}


ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately. Thank you.





On Jan 17, 2012, at 01:38, Will McLaren wrote:

> 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
> 
>> 
>> ॐ
>> 
>> Michael Yourshaw
>> 
>> UCLA Geffen School of Medicine
>> Department of Human Genetics, Nelson Lab
>> 695 Charles E Young Drive S
>> Gonda 5554
>> 
>> Los Angeles CA 90095-8348 USA
>> 
>> myourshaw at ucla.edu
>> 
>> 970.691.8299
>> 
>> This message is intended only for the use of the addressee and may contain
>> information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY
>> WORK PRODUCT. If you are not the intended recipient, you are hereby notified
>> that any dissemination of this communication is strictly prohibited. If you
>> have received this communication in error, please erase all copies of the
>> message and its attachments and notify us immediately. Thank you.
>> 
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
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>> 

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