[ensembl-dev] Required to use --fasta flag with --refseq?

[Will McLaren]

Hi Matt,

For the FASTA file to be found it needs to be in a specific directory,
namely [cache_dir]/[species]/[version]_[assembly]/ where [cache_dir]
defaults to $HOME/.vep/

For the refseq cache, the species name is altered to be e.g.
homo_sapiens_refseq/75/ ; the merged cache is similarly named
homo_sapiens_merged.

You should be able to symlink the files from your non-RefSeq homo_sapiens
cache;

ln -s [cache_dir]/homo_sapiens/75/*.fa* [cache_dir]/homo_sapiens_refseq/75/

HTH

Will McLaren
Ensembl Variation

On 3 February 2015 at 23:27, Matt Wood <matt.wood at codifiedgenomics.com>
wrote:

> I've installed the following caches:
>
> homo_sapiens_refseq_vep_75.tar.gz
> homo_sapiens_vep_75.tar.gz
>
> and the FASTA file for homo_sapiens.
>
> I'm trying to get access to the ref sequence from a VEP plugin when
> running with the refseq flag. I have no problems when running without the
> flag. My args are:
>
> -dir ~/.vep --force_overwrite --refseq -offline --vcf --plugin RSTest -i
> test.vcf -o test.out
>
> In my RSTest plugin I do the following:
>
> my $subslice = $vf->slice->sub_Slice($start, $end)->seq;
>
> But, my $subslice is always "NNNNNNNNNNN". If I remove the refseq flag I
> get what I expect.
>
> I found that if I add a --fasta flag and point explicitly to the fasta
> file that was downloaded by the VEP install process things work as expected.
>
> Is this expected behavior? Or is there some way for the fasta file to be
> recognized implicitly like when running without the refseq flag?
>
> Thanks.
>
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