from ete2 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']
from ete2 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 # /---| | |