<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
</head>
<body bgcolor="#ffffff" text="#000000">
Esteemed api developers,<br>
<br>
Is there any easy way with the perl api to tell if a known variant
(by this i mean one that has a an rsID and that i have created like
this:<br>
<br>
# Variation feature representing a single nucleotide polymorphism<br>
$vf = <b>Bio::EnsEMBL::Variation::VariationFeature</b>->new<br>
(-start => 100,<br>
-end => 100,<br>
-strand => 1,<br>
-slice => $slice,<br>
-allele_string => 'A/T',<br>
-variation_name => 'rs635421',<br>
-map_weight => 1,<br>
-variation => $v);<br>
<br>
is known to map to another region of the genome other than the
region have specified with the slice/start/end properties?<br>
<br>
dbSNP variants can be assigned to multiple genome locations when it
hasn't been possible to unambiguously assign them to a single
location.<br>
<br>
If i can't tell from the variation feature directly i believe i can
do this:<br>
<br>
$vfa = $reg->get_adaptor("human","variation","variationfeature");<br>
$va = $reg->get_adaptor("human","variation","variation");<br>
<br>
# fetch all genome hits for a particular variation <br>
$v = $va->fetch_by_name('rs56'); <br>
$count = @{$vfa->fetch_all_by_Variation($v)}<br>
if $count > 1 then it maps to more than one place? <br>
<br>
I was hoping to be able to do it directly from teh variation feature<br>
<br>
thanks<br>
<br>
</body>
</html>