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Hi Jan,<br>
<br>
Actually we use the script you mentionned
(/ensembl-variation/scripts/import/import_ega_sv_data.pl) to import
directly DGVa data from GVF files (e.g.
<a class="moz-txt-link-freetext" href="ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd1_Redon_et_al_2006/gvf/">ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd1_Redon_et_al_2006/gvf/</a>).<br>
<br>
I just implemented the method store in the HEAD code of the cvs:<br>
-
ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/BaseStructuralVariationAdaptor.pm<br>
- ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/StructuralVariationFeatureAdaptor.pm<br>
and a small fix in an other module (also in the HEAD code):<br>
- ensembl-variation/modules/Bio/EnsEMBL/Variation/BaseStructuralVariation.pm<br>
<br>
Please let me know if you still have some issues.<br>
<br>
Cheers,<br>
<pre class="moz-signature" cols="72">Laurent</pre>
<br>
On 20/03/2012 06:04, Jan Vogel wrote:
<blockquote
cite="mid:E7C60BAC-DE1C-45C9-9661-0065CC5A3A0C@gmail.com"
type="cite">
<div><br>
</div>
<div>Heya Ensembl,</div>
<div><br>
</div>
<div>I'm trying to import structural variations into a
ensembl-variation database. </div>
<div><br>
</div>
<div>Currently I am creating a
few Bio::EnsEMBL::Variation::StructuralVariationFeature()
objects and than add them to
the Bio::EnsEMBL::Variation::DBSQL::StructuralVariationFeatureAdaptor
- i tried to call the store() method but get an exception : </div>
<div><br>
</div>
<div>
<div><font class="Apple-style-span" face="Courier">--------------------
EXCEPTION --------------------</font></div>
<div><font class="Apple-style-span" face="Courier">MSG: Abstract
method store not defined by implementing subclass</font></div>
<div><font class="Apple-style-span" face="Courier"><br>
</font></div>
<div><font class="Apple-style-span" face="Courier">STACK
Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::store
…./ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm:1105</font></div>
<div><font class="Apple-style-span" face="Courier">STACK
toplevel import_structual_variation_data.pl:65</font></div>
<div><font class="Apple-style-span" face="Courier">Ensembl API
version = 66</font></div>
<div><font class="Apple-style-span" face="Courier">---------------------------------------------------</font></div>
</div>
<div><br>
</div>
<div>It seems that there's currently no API support to store
structural variations in an ensembl variation database. So, how
do these features get imported from DGVa into Ensembl ?</div>
<div><br>
</div>
<div>I came across a script :
/ensembl-variation/scripts/import/import_ega_sv_data.pl which
has a lot of raw sql in it - are you using this script ?</div>
<div><br>
</div>
<div><br>
</div>
<div>Ah, btw there's a bug in Bio::EnsEMBL::Registry for
branch-ensembl-66 -: the "end-comma" is missing in line 169 -
it's fixed in the trunk:</div>
<div><br>
</div>
<div><font class="Apple-style-span" face="Courier">cvs diff -r
HEAD -r 1.220 Registry.pm</font></div>
<div>…..</div>
<div><span class="Apple-style-span" style="font-family: Courier; "><
'vega' => 'Bio::EnsEMBL::DBSQL::DBAdaptor'</span><font
class="Apple-style-span" face="Courier">
<div>< 'vega_update' =>
'Bio::EnsEMBL::DBSQL::DBAdaptor',</div>
<div>---</div>
</font><span class="Apple-style-span" style="font-family:
Courier; ">> 'vega' =>
'Bio::EnsEMBL::DBSQL::DBAdaptor',</span><font
class="Apple-style-span" face="Courier">
<div>> 'vega_update' =>
'Bio::EnsEMBL::DBSQL::DBAdaptor',</div>
<div><br>
</div>
</font></div>
<div><br>
</div>
<div>Cheers, </div>
<div><br>
</div>
<div> Jan Vogel </div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div> </div>
<div><br>
</div>
<br>
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<br>
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</pre>
</blockquote>
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