from ete3 import PhylomeDBConnector
# This connects to the main phylomeDB server (default parameters)
p = PhylomeDBConnector()
# Obtains the phylomeDB internal ID for my gene of interest
idmatches = p.search_id("ENSG00000146556")
# Take the only match (several would be possible)
geneid = idmatches[0]
# Gets the 'geneid' tree in phylome 1 reconstructed using WAG evolutionary model
t, likelihood = p.get_tree(geneid, "WAG", 1)
print t
#
# /-Xtr0044988
# |
# | /-Gga0000980
# | |
# /---| | /-Bta0018700
# | | | |
# | | | | /-Hsa0000001
# | | | | /---|
# | | | /---| /---| \-Hsa0010733
# | \---| | | | |
# | | | | /---| \-Hsa0010710
# | | | | | |
# | | /---| \---| \-Ptr0000001
# /---| | | | |
# | | | | | \-Cfa0016699
# | | | | |
# | | \---| | /-Rno0030248
# | | | \---|
# | | | \-Mms0024821
# /---| | |
from ete3 import PhylomeDBConnector
# This connects to the main phylomeDB server (default parameters)
p = PhylomeDBConnector()
# Obtains the phylomeDB internal ID for my gene of interest
idmatches = p.search_id("ENSG00000146556")
# Take the only match (several would be possible)
geneid = idmatches[0]
# Gets the 'geneid' tree in phylome 1 reconstructed using WAG evolutionary model
t, likelihood = p.get_tree(geneid, "WAG", 1)
print t
#
# /-Xtr0044988
# |
# | /-Gga0000980
# | |
# /---| | /-Bta0018700
# | | | |
# | | | | /-Hsa0000001
# | | | | /---|
# | | | /---| /---| \-Hsa0010733
# | \---| | | | |
# | | | | /---| \-Hsa0010710
# | | | | | |
# | | /---| \---| \-Ptr0000001
# /---| | | | |
# | | | | | \-Cfa0016699
# | | | | |
# | | \---| | /-Rno0030248
# | | | \---|
# | | | \-Mms0024821
# /---| | |
