[ensembl-dev] Fwd: Retrieving CAFE gene tree data...

Steve Moss gawbul at gmail.com
Thu Jun 6 13:55:08 BST 2013


Dear EnsEMBL developers,

I'm trying to work out how best to retrieve a tree (Newick format?) showing
the significant expansions and contractions, as you can see here, for
example
http://www.ensembl.org/Homo_sapiens/Gene/SpeciesTree?db=core;g=ENSG00000159917;r=19:44782947-44813601;t=ENST00000291182
.

I'm playing around with the API at the moment and pulling some data out,
but it isn't that intuitive. The current CAFEGeneFamily and
CAFEGeneFamilyAdaptor code doesn't seem to have any examples on this and I
can't find anything in the EnsEMBL tutorial information.

I've been through all my candidate genes, pulled the CAFE gene tree root
IDs for those data, that have a significant CAFE gene gain/loss tree, but
am struggling with where to go from there to build the final "product" i.e.
a text representation of the above graphic?

Ideally, I would like to be able to output this in a CAFE style output
format (EnsEMBL Family ID, Gene Tree (with species name and gene count),
Family P Value, Nodes P Values), e.g.:

ENSFM00250000006933
(((((((((Homosapiens_7:6.4,Pantroglodytes_1:6.4)_1:2.4,Gorillagorilla_1:8.8)_1:6.9,Pongoabelii_1:15.7)_1:4.7,Nomascusleucogenys_1:20.4)_1:8.8,Macacamulatta_1:29.2)_1:13.4,Callithrixjacchus_1:42.6)_1:22.6,Tarsiussyrichta_0:65.2)_1:8.8,(Microcebusmurinus_1:57.9,Otolemurgarnettii_1:57.9)_1:16.1)_1:16,Tupaiabelangeri_1:90)_1
0.004000
((0.000000,0.538467),(0.513088,0.543748),(0.534524,0.597471),(0.524517,0.585395),(0.544478,0.583311),(0.568740,0.701965),(0.613489,0.272744),(0.541873,0.581644),(0.675047,0.563343),(0.591851,0.503703))

Has anyone done this already?

Kindest regards,

Steve Moss
http://about.me/gawbul
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20130606/71da819e/attachment.html>


More information about the Dev mailing list