<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Rob,<div class=""><br class=""></div><div class="">I won’t ever say it cannot be done just in the database. More I don’t think it’ll be as performant or as easy as the alternatives myself & Kieron suggested :).</div><div class=""><br class=""></div><div class="">Andy</div><div class=""><br class=""><div apple-content-edited="true" class="">
------------<br class="">Andrew Yates - Ensembl Support Coordinator<br class="">European Molecular Biology Laboratory<br class="">European Bioinformatics Institute<br class="">Wellcome Trust Genome Campus<br class="">Hinxton, Cambridge<br class="">CB10 1SD, United Kingdom<br class="">Tel: +44-(0)1223-492538<br class="">Fax: +44-(0)1223-494468<br class="">Skype: andrewyatz<br class=""><a href="http://www.ensembl.org/" class="">http://www.ensembl.org/</a>
</div>
<br class=""><div><blockquote type="cite" class=""><div class="">On 16 Dec 2014, at 16:40, Rob Sargent <<a href="mailto:rob.sargent@utah.edu" class="">rob.sargent@utah.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<font size="-1" class=""><font face="Courier New, Courier, monospace" class="">A
function/stored-procedure using a recursive CTE might be the way
for Steve to go.<br class="">
<br class="">
</font></font>
<div class="moz-cite-prefix">On 12/16/2014 09:28 AM, Andrew Yates
wrote:<br class="">
</div>
<blockquote cite="mid:469F4D6A-436C-46C2-9340-535201787788@ebi.ac.uk" type="cite" class="">
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Hey Steve,
<div class=""><br class="">
</div>
<div class="">The problem with using the database is that sequence
is not stored against the top-level sequences annotation is held
against. Instead sequence is held against the contig sequence
regions which requires descending through the assembly table an
unspecified number of times (once for each mapping e.g.
chromosome -> supercontig -> contig). </div>
<div class=""><br class="">
</div>
<div class="">I would seriously *not* recommend doing this. Not
only do you have to deal with descending down the assembly but
also having to think about concatenating the sequence &
paying attention to the orientation of assembly. Instead you
could use the Perl API (probably not an option considering
you’re a Python guy), BioMart (you can access unspliced gene
sequence quite easily), the REST API or download the full genome
sequence from FTP and doing subslices. The faindex index tool
from htslib/samtools is pretty good at extracting arbitrary
sequence from very large FASTA files.</div>
<div class=""><br class="">
</div>
<div class="">Andy</div>
<div class=""><br class="">
</div>
<div apple-content-edited="true" class="">
------------<br class="">
Andrew Yates - Ensembl Support Coordinator<br class="">
European Molecular Biology Laboratory<br class="">
European Bioinformatics Institute<br class="">
Wellcome Trust Genome Campus<br class="">
Hinxton, Cambridge<br class="">
CB10 1SD, United Kingdom<br class="">
Tel: +44-(0)1223-492538<br class="">
Fax: +44-(0)1223-494468<br class="">
Skype: andrewyatz<br class="">
<a moz-do-not-send="true" href="http://www.ensembl.org/" class="">http://www.ensembl.org/</a>
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<br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 16 Dec 2014, at 16:15, Steve Moss <<a moz-do-not-send="true" href="mailto:gawbul@gmail.com" class="">gawbul@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class=""><span style="font-size:13px" class="">Dear EnsEMBL Dev,</span>
<div dir="ltr" style="font-size:13px" class="">
<div class=""><br class="">
</div>
<div class="">I'm trying to write a raw SQL query to
retrieve the sequence for the human BRCA2 gene to
compare different methods of accessing EnsEMBL data.
I'm currently doing the following, but getting an
empty set.</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">SELECT SUBSTRING(sequence,
g.seq_region_start, g.seq_region_end)</div>
<div class="">FROM dna d</div>
<div class="">JOIN gene g</div>
<div class="">ON d.seq_region_id = g.seq_region_id</div>
<div class="">WHERE g.stable_id="ENSG00000139618"</div>
</div>
<div class=""><br class="">
</div>
<div class="">What am I missing? I think I'm falling
short on working out the coord. system mapping stuff.
Any pointers to help in fixing please?</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class=""><br class="">
Steve</div>
</div>
<div class=""><br class="">
</div>
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