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Hi Will<br>
<br>
Just to be 100% clear about this answer, are you saying that methods
that return more than one object don't return failed variants (in
v61 and all previous versions) but in v61 you can call the method
include_failed_variations on the adaptors? If i am reading that
right you dont need to check the data returned by the adaptors for
failed variants as they are excluded by default.<br>
<br>
On 07/02/2011 13:48, Will McLaren wrote:
<blockquote
cite="mid:AANLkTi=s=GinYw8f=me7dyTmT38BvkQXChQSPrLz_-g1@mail.gmail.com"
type="cite">Hello Gavin,
<div><br>
</div>
<div>We apply some QC checking to the data that we import - we can
assign variations a status of "failed", along with a description
of why this has happened. You can access this through a
variation object using the failed_description() method. The list
Andrea gave is the list of all possible failed descriptions.</div>
<div><br>
</div>
<div>The API is configured such that by default data associated
with failed variations are not returned by methods that return
more than one object (e.g. fetch_all_by_Slice in
VariationFeatureAdaptor); you can force the retrieval of such
data by retrieving the variation directly (e.g. using
fetch_by_name in VariationAdaptor), or by calling the method
include_failed_variations() on any adaptor from the Variation
group (functionality only available from e!61 onwards).</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
</div>
<div>Will</div>
<div><br>
<br>
<div class="gmail_quote">On 7 February 2011 09:29, Oliver, Gavin
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:gavin.oliver@almacgroup.com">gavin.oliver@almacgroup.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div link="blue" vlink="blue" lang="EN-US">
<div>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt; font-family:
Arial; color: navy;">Those were the statuses I was
referring to Will.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt; font-family:
Arial; color: navy;"> </span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt; font-family:
Arial; color: navy;">Which leads me to ask – what
were the statuses that Andrea listed?</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt; font-family:
Arial; color: navy;"> </span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt; font-family:
Arial; color: navy;">Gavin</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt; font-family:
Arial; color: navy;"> </span></font></p>
<div>
<div class="MsoNormal" style="text-align: center;"
align="center"><font face="Times New Roman" size="3"><span
style="font-size: 12pt;">
<hr width="100%" align="center" size="2"> </span></font></div>
<p class="MsoNormal"><b><font face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma;
font-weight: bold;">From:</span></font></b><font
face="Tahoma" size="2"><span style="font-size:
10pt; font-family: Tahoma;"> <a
moz-do-not-send="true"
href="mailto:dev-bounces@ensembl.org"
target="_blank">dev-bounces@ensembl.org</a>
[mailto:<a moz-do-not-send="true"
href="mailto:dev-bounces@ensembl.org"
target="_blank">dev-bounces@ensembl.org</a>] <b><span
style="font-weight: bold;">On Behalf Of </span></b>Will
McLaren<br>
<b><span style="font-weight: bold;">Sent:</span></b>
04 February 2011 15:04<br>
<b><span style="font-weight: bold;">To:</span></b>
Andrea Edwards<br>
<b><span style="font-weight: bold;">Cc:</span></b>
<a moz-do-not-send="true"
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
<b><span style="font-weight: bold;">Subject:</span></b>
[SPAM] - Re: [ensembl-dev] Transcript variation
alleles - - Bayesian Filter detected spam</span></font></p>
</div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;"> </span></font></p>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;">Hello,</span></font></p>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;">I think
there are some crossed wires here -
validation_status is a property of a variation
supplied to us by dbSNP.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;">Their
descriptions are here:</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;"><a
moz-do-not-send="true"
href="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_legend.cgi?legend=validation"
target="_blank">http://www.ncbi.nlm.nih.gov/projects/SNP/snp_legend.cgi?legend=validation</a><br>
<br>
The pictures are, in order:</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;">cluster</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;">freq</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;">submitter</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;">doublehit</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;">hapmap</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;">1000Genome</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;"> </span></font></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;"><font
face="Times New Roman" size="3"><span
style="font-size: 12pt;">Will</span></font></p>
<div>
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;">On 4
February 2011 14:14, Andrea Edwards <<a
moz-do-not-send="true"
href="mailto:edwardsa@cs.man.ac.uk"
target="_blank">edwardsa@cs.man.ac.uk</a>>
wrote:</span></font></p>
<div text="#000000" bgcolor="#ffffff">
<p class="MsoNormal"><font face="Times New Roman"
size="3"><span style="font-size: 12pt;"><br>
Gavin<br>
<br>
I believe the validatation statuses are just
pass and fail <br>
<br>
If you query the variation schema directly
you can find the reasons for failure when a
variation is imported from say dbSNP<br>
<br>
mysql> select description from
failed_description;<br>
+--------------------------------------------------------+<br>
|
description
|<br>
+--------------------------------------------------------+<br>
| Variation maps to more than 3 different
locations |<br>
| None of the variant alleles match the
reference allele |<br>
| Variation has more than 3 different
alleles |<br>
| Loci with no observed variant alleles in
dbSNP |<br>
| Variation does not map to the
genome |<br>
| Variation has no associated
sequence |<br>
+--------------------------------------------------------+<br>
6 rows in set (0.06 sec)<br>
<br>
As will has said, they map all variants to
the positive strand and make sure at least
one of the variant alleles exists at the
base position in the forward strand. If this
failed you would get the error 'None of the
variant alleles match the reference allele.'
I think the others are fairly self
explanatory though i'm not sure how a
variant could have no associated sequence if
it was imported from dbSNP<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 02/02/2011 15:20, Oliver, Gavin wrote: </span></font></p>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Thanks Graham - </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Can you also tell me where to find information on the meaning of the</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">possible validation statuses?</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">-----Original Message-----</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">From: Graham Ritchie [<a moz-do-not-send="true" href="mailto:grsr@ebi.ac.uk" target="_blank">mailto:grsr@ebi.ac.uk</a>] </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Sent: 02 February 2011 15:12</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">To: Oliver, Gavin</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Cc: <a moz-do-not-send="true" href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a></span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Subject: [SPAM] - Re: [ensembl-dev] Transcript variation alleles - Email</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">found in subject</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Hi Gavin,</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">The alleles of a transcript variation always represent the genomic base</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">change.</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Cheers,</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Graham</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Ensembl variation</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">On 2 Feb 2011, at 15:02, Oliver, Gavin wrote:</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<blockquote style="margin-top: 5pt; margin-bottom:
5pt;" type="cite">
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Hi,</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">When I pull transcript variation alleles via the API, does the allele</span></font></pre>
</blockquote>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">shown (e.g. A/T) represent the genomic base change, or the</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">transcriptomic one?</span></font></pre>
<blockquote style="margin-top: 5pt; margin-bottom:
5pt;" type="cite">
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Gavin</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"> </span></font></pre>
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<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">message in error, you should delete it from your system immediately and</span></font></pre>
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<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Almac Group (UK) Limited, registered no. NI061368. Almac Sciences</span></font></pre>
</blockquote>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Limited, registered no. NI041550. Almac Discovery Limited, registered</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">no. NI046249. Almac Pharma Services Limited, registered no. NI045055.</span></font></pre>
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<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac</span></font></pre>
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<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are</span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">Delaware</span></font> limited liability companies and Almac Group Incorporated is a</pre>
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(UK) Limited, registered no. NI061368.<span> </span>Almac
Sciences Limited, registered no. NI041550.<span>
</span>Almac Discovery Limited, registered no.
NI046249. <span> </span>Almac Pharma Services
Limited, registered no. NI045055.<span> </span>Almac
Clinical Services Limited, registered no.
NI041905.<span> </span>Almac Clinical
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</span>All preceding companies are registered in
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