<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi Gang,<br>
<br>
We found the same number of variations using the SQL query, API
calls (and also the Ensembl Transcript web pages, which uses the
API).<br>
Which methods did you use for your perl script ?<br>
To test the data, I used the script below:<br>
<br>
use strict;<br>
use warnings;<br>
use Bio::EnsEMBL::Registry;<br>
<br>
my $registry = 'Bio::EnsEMBL::Registry';<br>
$registry->load_registry_from_db(<br>
-host => 'ensembldb.ensembl.org',<br>
-user => 'anonymous'<br>
);<br>
<br>
my $so_term = 'insertion';<br>
my $t_adaptor = $registry->get_adaptor('human', 'core',
'transcript');<br>
my $tv_adaptor = $registry->get_adaptor('human', 'variation',
'transcriptvariation');<br>
<br>
my @transcripts;<br>
foreach my $t
('ENST00000419234','ENST00000327551','ENST00000547043','ENST00000539060')
{<br>
push @transcripts, $t_adaptor->fetch_by_stable_id($t);<br>
}<br>
<br>
my %variations;<br>
foreach my $tv
(@{$tv_adaptor->fetch_all_by_Transcripts(\@transcripts)}) {<br>
if ($tv->variation_feature->class_SO_term eq $so_term) {<br>
$variations{$tv->variation_feature->variation_name} =
1;<br>
}<br>
}<br>
print "Count: ". scalar (keys %variations)."\n";<br>
<br>
Cheers,<br>
<pre class="moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
On 14/08/2012 10:17, 陈岗 wrote:<br>
</div>
<blockquote
cite="mid:CABjKtWZNFTUi=TLP+GEuzTdsMSs-kDP0B42S1XizmRdifMJoew@mail.gmail.com"
type="cite">Hi All
<div><br>
</div>
<div>I got variation IDs with SQL sentences, but their numbers are
inconsistent with the result from API.</div>
<div><br>
</div>
<div>For example, my SQL counts gene ENSG00000089234 has 38
insertions, 45 deletions, 5 indels, 0 substitution. However,
Ensembl API read out 30 insertions, 40 deletions 1
substitutions.</div>
<div><br>
</div>
<div>If anyone know the reason that causes the difference, please
tell me. Thanks</div>
<div><br>
</div>
<div>My SQL for insertion:</div>
<div><br>
</div>
<div>( SELECT att.value,vf.variation_name</div>
<div>FROM transcript_variation tv</div>
<div>LEFT JOIN variation_feature vf ON ( vf.variation_feature_id =
tv.variation_feature_id ) </div>
<div>LEFT JOIN attrib att ON ( att.attrib_id = vf.class_attrib_id
) </div>
<div>WHERE tv.feature_stable_id = 'ENST00000419234'</div>
<div> AND att.value = 'insertion' )</div>
<div><br>
</div>
<div>union</div>
<div><br>
</div>
<div>
<div>( SELECT att.value,vf.variation_name</div>
<div>FROM transcript_variation tv</div>
<div>LEFT JOIN variation_feature vf ON ( vf.variation_feature_id
= tv.variation_feature_id ) </div>
<div>LEFT JOIN attrib att ON ( att.attrib_id =
vf.class_attrib_id ) </div>
<div>WHERE tv.feature_stable_id = 'ENST00000327551'</div>
<div> AND att.value = 'insertion' )</div>
</div>
<div><br>
</div>
<div>
<div>
union</div>
<div><br>
</div>
<div>
<div>( SELECT att.value,vf.variation_name</div>
<div>FROM transcript_variation tv</div>
<div>LEFT JOIN variation_feature vf ON (
vf.variation_feature_id = tv.variation_feature_id ) </div>
<div>
LEFT JOIN attrib att ON ( att.attrib_id = vf.class_attrib_id
) </div>
<div>WHERE tv.feature_stable_id = 'ENST00000547043'</div>
<div> AND att.value = 'insertion' )</div>
</div>
<div><br>
</div>
<div>
<div>union</div>
<div><br>
</div>
<div>
<div>( SELECT att.value,vf.variation_name</div>
<div>FROM transcript_variation tv</div>
<div>LEFT JOIN variation_feature vf ON (
vf.variation_feature_id = tv.variation_feature_id ) </div>
<div>LEFT JOIN attrib att ON ( att.attrib_id =
vf.class_attrib_id ) </div>
<div>WHERE tv.feature_stable_id = 'ENST00000539060'</div>
<div> AND att.value = 'insertion' )</div>
</div>
</div>
<div><br>
</div>
<div><br>
</div>
-- <br>
<div><font face="verdana, sans-serif" size="1">Gang Chen</font></div>
<div><font face="verdana, sans-serif" size="1">TILSI</font></div>
<div><font face="verdana, sans-serif" size="1"><span
style="background-color:rgb(255,255,255)">Taicang
Institute For Life Science Information</span><br
style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255)">Address:
A2/162, Renmin South Road, Taicang, 215400, Jiangsu
Province, P.R.China</span><br
style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255)">Phone:
（+86）512-82782588</span></font></div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
List admin (including subscribe/unsubscribe): <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>