def _sorted_homologenes(self, homologenes):
'''sort list of homologenes [(taxid, geneid),...] based on the order
defined in species_li.
'''
d = {}
for i, species in enumerate(list(TAXONOMY.keys())):
d[TAXONOMY[species]["tax_id"]] = i
gene_li = [(d.get(taxid, taxid), taxid, geneid)
for taxid, geneid in homologenes]
return [g[1:] for g in sorted(gene_li)]
def __init__(self, data_folder):
# if species_li is None, include all species
self.set_species_li(list(TAXONOMY.keys()))
self.data_folder = data_folder
self.datafile = os.path.join(self.data_folder, self.DATAFILE)