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
# /---| | |
from ete3 import PhylomeDBConnector
# This connects to the main phylomeDB server (default parameters)
p = PhylomeDBConnector()
# Obtains a list of available phylomes
phylomes_list = p.get_phylomes()
# Obtains the list of proteomes used in phylome 1 (the human phylome)
phylomes_list = p.get_proteomes_in_phylome(1)
# all seeds (potentially, trees) in the human phylome
all_seed_sequences = p.get_seed_ids(1)
# Gets species info from associated to the "Hsa" code
print p.get_species_info("Hsa")
# {'code': 'Hsa', 'taxid': 9606L, 'name': 'Homo_sapiens'}
#
# You can also use the same method to find the species code given a ncbi taxid
print p.get_species_info(9606)
# {'code': 'Hsa', 'taxid': 9606L, 'name': 'Homo_sapiens'}
#
# Get phylomeDB IDs matching a given Ensembl protein ID. Always
# returns the code of the longest isoform.
idmatches = p.search_id("ENSG00000146556")
# You can also use the search_id method to find the longest isoform of
# the gene associated to a given phylomeID. Note that phylomeDB trees
# are always reconstructed using the longest isoform associated to a
# gene.
#
print p.search_id("Hsa0000125")
# ['Hsa0000122']
