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Hi Simon,<br>
<br>
For ensembl genomes species, we recommend using the LookUp method as
described here:<br>
<a class="moz-txt-link-freetext" href="http://bacteria.ensembl.org/info/data/accessing_ensembl_bacteria.html#intro">http://bacteria.ensembl.org/info/data/accessing_ensembl_bacteria.html#intro</a><br>
<br>
For a given registry, you can use the 'get_all_by_name_pattern'
method for approximate matching.<br>
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<pre class="code" style="font-family: 'Courier New', Courier, monospace; font-size: 13px; margin: 0px 0px 16px; border: 1px solid rgb(204, 204, 204); background-color: rgb(240, 240, 240); padding: 8px !important; line-height: 16px; color: rgb(85, 85, 85); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-position: initial initial; background-repeat: initial initial;">my $lookup = Bio::EnsEMBL::LookUp->new(-URL=><a class="moz-txt-link-rfc2396E" href="http://bacteria.ensembl.org/registry.json">"http://bacteria.ensembl.org/registry.json"</a>,-NO_CACHE=>1);
my @dbas = @{$lookup->get_all_by_name_pattern('escherichia_coli_.*')};</pre>
or by taxon id<br>
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<pre class="code" style="font-family: 'Courier New', Courier, monospace; font-size: 13px; margin: 0px 0px 16px; border: 1px solid rgb(204, 204, 204); background-color: rgb(240, 240, 240); padding: 8px !important; line-height: 16px; color: rgb(85, 85, 85); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-position: initial initial; background-repeat: initial initial;">my @dbas = @{$lookup->get_all_by_taxon_id(388919)};
</pre>
If it still fails to find the species you are looking for, I would
try running the ping_ensembl.pl script to make sure you are
connecting to the right databases.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 24/02/2014 12:03, Simon Andrews
wrote:<br>
</div>
<blockquote
cite="mid:E64B2A778028AB4A8EA6EB700647BFF601FA1C7F69@MAIL1.babraham.ac.uk"
type="cite">
<pre wrap="">I have a script which used to go through all possible adapters in the registry to give me a choice of genomes to process. However in recent ensemblgenomes releases this no longer works as it takes so long to get through the thousands of adapters that it never completes.
I'm therefore trying to set up a specific slice adapter for the species I want. The problem is I can't find the correct name to use and I don't know how to get it. I'm trying to work with the latest S pombe release and my adapter setup looks like this:
$slice_adapter = $registry->get_adaptor($species,'Core','Slice');
..I've tried various things in $species "S pombe" "Schizosaccharomyces pombe" "yeast" and probably some others, but all of them return MSG: S pombe is not a valid species name (check DB and API version).
How do I find the correct name to use for any given species?
Thanks
Simon.
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</pre>
</blockquote>
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