<div dir="ltr">I did download a FASTA with the installer and am already using the --offline flag.<div><br></div><div>I've got a version mostly working now where I do the following:</div><div><br></div><div>1. Get start and end positions using Bio::EnsEMBL::Variation::TranscriptVariation::cdna_start and Bio::EnsEMBL::Variation::TranscriptVariation::cdna_end</div><div>2. Convert those to genomic coordinates using Bio::EnsEMBL::TranscriptMapper::cdna2genomic</div><div>3. Loop through the returned coords and concat the sequence using Bio::EnsEMBL::Slice::sub_Slice</div><div><br></div><div>I'm a little concerned there may be some corner cases I'm missing that Bio::EnsEMBL::Transcript::spliced_seq was handling, but so far I haven't run into that. And it's fast enough.</div><div><br></div><div>Matt Wood</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Nov 13, 2014 at 11:07 PM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Matt,<div><br></div><div>I assume you're already using a FASTA file (<a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#fasta" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#fasta</a>).</div><div><br></div><div>There does seem to be some issue with the sequence fetching code, however. If you are using the VEP's --offline flag then the issue doesn't appear (at least for me). If you use --cache (which asks the code to prefer use of offline resources including the FASTA file but still allows connections to the DB) then in this particular case calling that method seems to bypass the code that fetches sequence from the FASTA file and instead fetches it from the DB.</div><div><br>While we look into this issue, can you possibly try using --offline if you aren't already?</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On 13 November 2014 07:39, Matt Wood <span dir="ltr"><<a href="mailto:matt.wood@codifiedgenomics.com" target="_blank">matt.wood@codifiedgenomics.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">I'm working on a VEP plugin where I need to look at a section of cDNA around the variant.<div><br></div><div>In a previous plugin, where I needed to do something similar with genomic DNA, I was able to get a slice from the VariationFeature and subslice it like this:</div><div><br></div><div>my $subseq = $vf->slice->sub_Slice($start, $end)->seq;<br></div><div><br></div><div>That worked really well and performed really well.</div><div><br></div><div>I can't find anything similar for the cDNA so I'm getting the spliced sequence from the transcript and then using substr() to do what sub_Slice did above.</div><div><br></div><div><div>my $cdna_seq = $transcript->spliced_seq;</div><div>my $subseq = substr($cdna_seq, $start, $end);</div></div><div><br></div><div>It works well enough, but performance is too poor to be useful, taking 2 or 3 seconds to get $subseq per transcript. I'm wondering if I'm going about things the wrong way and am skipping a cache or something with the methods I'm using.</div><div><br></div><div>Any ideas for how I can get better performance? Is there a better way to get a chunk of a transcript's spliced sequence?</div><div><br></div><div>Thanks,</div><div>Matt Wood</div><div>Codified Genomics</div></div>
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