Hi Andrea,<div><br></div><div>The Iterator code is indeed a new addition that we introduced in release 61 in order to handle this kind of cases that will otherwise typically break the API. So far we have only implemented them in a few places but we will keep adding these where we think it is motivated and desired.</div>
<div><br></div><div>I can't say exactly which of your approaches is best and it may depend on your downstream application but also the size of the set. If, for example, you need the mapping of the variation and it is logical for you to retrieve them according to the position along the chromosome, your first approach might be best. That is, unless you expect the set to be relatively small or unevenly distributed across the genome (this would not typically be the case for the Watson or 1000 genomes data). Currently, you can only use the iterator for the second approach.<br>
</div><div><br></div><div>/Pontus</div><div><br></div><div><br><div class="gmail_quote">2011/3/2 Andrea Edwards <span dir="ltr"><<a href="mailto:edwardsa@cs.man.ac.uk">edwardsa@cs.man.ac.uk</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff">
HI Pontus<br>
<br>
I did in fact run out of memory every time! I wasn't aware of any
sort of iterator on the api. Are they new as i don't remember them
when i read teh tutorials late last year?<br>
<br>
Do you have any comments about which of my 2 approaches is best? I
presume you can use an iterator on the second approach as that is
basically the code you supplied (minus an iterator). Could you use
an iterator on the first approach?<br>
<br>
thanks<div><div></div><div class="h5"><br>
<br>
On 02/03/2011 15:22, Pontus Larsson wrote:
<blockquote type="cite">Hi Chris,
<div><br>
</div>
<div>Andrea is right, we have grouped these variations together
into various variation sets. For example, you can get all
variations belonging to the different pilots from the sets '1000
genomes - Low coverage', '1000 genomes - High coverage - Trios'
and '1000 genomes - High coverage exons' for pilot 1,2 and 3,
respectively. You'll need to use the VariationSet and
VariationSetAdaptor modules for this. It is not possible to
retrieve the variations conditional on submission date. </div>
<div><br>
</div>
<div>As Andrea points out, if you call the 'get_all_Variations'
method on a VariationSet object, the API will create all
variation objects and return them. For large sets like these,
this can easily cause you to run out of memory but you can use
the 'get_Variation_Iterator' method to get an Iterator object
and iterate over the variations instead. </div>
<div><br>
</div>
<div>/Pontus</div>
<div><br>
</div>
<div><span style="font-family:'courier new',monospace"> </span></div>
<div><br>
<div class="gmail_quote">2011/3/2 <span dir="ltr"><<a href="mailto:cj5@sanger.ac.uk" target="_blank">cj5@sanger.ac.uk</a>></span><br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
Hi,<br>
Is it possible using the variations API to get a list of
SNPS which have<br>
been submitted from the 1000 Genomes project?<br>
<br>
I have a vague idea that it should be possible to retrieve
such a list<br>
using the SS (submission) ID and/or the validation status,
however I am<br>
unsure of the details and what version of the API should be
used.<br>
<br>
The latest 100 genomes pilot release (2010_07) would be
great, but any<br>
earlier release would also be useful.<br>
<br>
Thanks<br>
Chris<br>
<br>
<br>
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