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)