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<div class="moz-cite-prefix">Have a look here:
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<a
href="http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Homology.html">http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Homology.html</a><br>
<br>
there you can find the documentation to the methods.<br>
<br>
M<br>
<br>
<br>
On 30/08/12 14:05, Yuan Chen wrote:<br>
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cite="mid:8C59FBA6-FFEA-4D6F-B866-3A330793FDBE@sanger.ac.uk"
type="cite">
<pre wrap="">On the same line, can any one explain what is n and s obtained by :
$homology->n; $homology->s;
Is this a number of non_synonymous or synonymous changes for the gene ?
yuan
On 30 Aug 2012, at 09:16, Matthieu Muffato wrote:
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<pre wrap="">Dear Mei
It seems that you are querying a fruit-fly gene. Unfortunately, the dN/dS values are only computed for close enough species: mammals, reptiles, and tetraodontiformes.
Nevertheless, your script is correct and would print some values if you use a human gene as query
Regards,
Matthieu
On 30/08/12 01:49, JiangMei wrote:
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<pre wrap="">Hi All.
Sorry to bother you. I'm trying to use ensembl-compara (database version
67) to extract the homologues. I also want to get the dN, dS and dN/dS.
However, ENSEMBL can't output these values. Can anyone help me?
The following is the script I used:
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host =>'ensembldb.ensembl.org',
-user =>'anonymous',
-db_version =>'67');
my $member_adaptor=$registry->get_adaptor('Multi','compara','Member');
my
$member=$member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE','FBgn0002780');
my $homology_adaptor=$registry->get_adaptor('Multi','compara','Homology');
my $homologies=$homology_adaptor->fetch_all_by_Member($member);
for $homology(@{$hom ologies}){
for $mem(@{$homology->get_all_Members}){
my $taxon=$mem->taxon; #check Bio::EnsEMBL::Compara::NCBITaxon
for methods
my $id=$mem->stable_id;
print "$id\t",$taxon->taxon_id,"\t",$taxon->genus,"
",$taxon->species,"\t";
}
print $homology->description,"\t",$homology->subtype,"\t";
my $dn=$homology->dn;
my $ds=$homology->ds;
my $dnds=$homology->dnds_ratio;
my $lnl=$homology->lnl;
($dn)?print "$dn\t$ds\t$dnds\t$lnl\n":print OUT "NA\tNA\tNA\tNA\n";
}
Wish your help! Thanks very much in advance!
Best, Mei
</pre>
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<pre wrap="">
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