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<font size="-1"><font face="Courier New, Courier, monospace">I don't
know which server you are using but I had these do amazing
things, and amazingly fast. Try it, you might like it. :)<br>
<br>
rjs<br>
<br>
</font></font>
<div class="moz-cite-prefix">On 12/16/2014 09:58 AM, Andrew Yates
wrote:<br>
</div>
<blockquote
cite="mid:9150285E-9F20-4B7F-8BDB-C71221528742@ebi.ac.uk"
type="cite">
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charset=windows-1252">
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 moz-do-not-send="true" 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
moz-do-not-send="true"
href="mailto:rob.sargent@utah.edu" class="">rob.sargent@utah.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class=""> <font
class="" size="-1"><font class="" face="Courier New,
Courier, monospace">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=""> 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>
</div>
<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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