[ensembl-dev] Bio::EnsEMBL::Feature::strand doesn't match output strand in plugin

[Matt Wood]

Thanks, that clears up my misunderstanding.

Matt Wood

On Wed, Oct 22, 2014 at 3:30 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Matt,
>
> The strand in $line_hash->{Extra}->{STRAND} is the strand of the
> overlapping genomic feature (transcript, regulatory feature etc), not the
> variation feature itself.
>
> It should match $tva->feature->strand in your example code.
>
> If your input is VCF, you will find that the strand of the variation
> feature is _always_ 1, as all variants encoded in VCF are on the forward
> strand.
>
> If the variation feature overlaps a transcript on the negative strand,
> then before any sequence annotation is done on the variant allele, it is
> reverse complemented; you can see the difference between the alleles in
> these situations by calling:
>
> # variant allele sequence relative to transcript
> $tva->feature_seq()
>
> # "original" variant allele sequence from variation feature
> $tva->variation_feature_seq()
>
> HTH
>
> Will McLaren
> Ensembl Variation
>
> On 21 October 2014 21:34, Matt Wood <matt.wood at codifiedgenomics.com>
> wrote:
>
>> I'm writing a plugin and am running into an issue with strand. The strand
>> I get from Bio::EnsEMBL::Feature::strand doesn't match the strand I'm
>> seeing in the output or the strand that is in the line hash provided to my
>> run method. Specifically I'm having an issue with the negative strand.
>>
>> This is my test plugin:
>>
>> package StrandTest;
>> use strict;
>> use warnings;
>> use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
>> use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
>>
>> sub run {
>>     my ($self, $tva, $line_hash) = @_;
>>
>>     my $strand = $tva->variation_feature->strand;
>>     my $extra_strand = $line_hash->{Extra}->{STRAND};
>>
>>     print("Strand: $strand/$extra_strand\n");
>>
>>     return {};
>> }
>>
>> 1;
>>
>> My output shows this: "Strand: 1/-1"
>>
>> The strand written to my output file is -1, and the strand in the line
>> hash is -1, but the strand from the VariationFeature is 1.
>>
>> My VCF:
>>
>> ##fileformat=VCFv4.0
>> #CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT
>> PAT
>> 6    133078809    .    C    A    60    PASS    .    GT:VR:RR:DP:GQ
>> 0/1:12:15:27:.
>>
>> I'm running VEP with these options: --plugin StrandTest --offline --vcf
>> --force_overwrite --pick -i test.vcf -o test.vep
>>
>> Any idea what's going on? For the time being I'm going to use
>> "$line_hash->{Extra}->{STRAND}" for my strand info. Is that safe to do? Are
>> there going to be cases where that hash is undef?
>>
>> Thanks,
>> Matt Wood
>>
>>
>>
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>
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