def __init__(self, config, taxonomy_fname):
self.config = config
self.taxonomy = GGTaxonomyFile(taxonomy_fname)
self.max_level = self.taxonomy.max_rank_level()
self.stats = [StatEntry() for i in range(self.max_level + 1)]
self.totstat_lvl = None
self.miss_list = []
self.tp = []
self.tn = []
self.fp = []
self.fn = []
for mis_rec in mislabel_map.itervalues():
rank = mis_rec["mis_rank"]
rank_mis_map[rank] = rank_mis_map.get(rank, 0) + 1
rank_mis_count = sorted(rank_mis_map.items(), key=itemgetter(0))
total = 0
for rank, cnt in rank_mis_count:
total += cnt
# print "%s:\t%d\t%d" % (rank,cnt,total)
print ""
if not args.gtruth_fname:
sys.exit(0)
true_taxonomy = GGTaxonomyFile(args.gtruth_fname)
out_path, out_stem = os.path.split(args.mis_fname)
if args.output_dir:
out_path = args.output_dir
if out_stem.endswith(".mis"):
out_stem = out_stem[:-4]
# mis_fname = os.path.join(out_path, out_stem + ".mis")
e = EpataxEvaluator(config, args.taxonomy_fname)
e.calc_mislabel_stats(mislabel_map, true_taxonomy.seq_ranks_map, False)
fp_fname = os.path.join(out_path,
out_stem + ".eval%d.fp" % int(args.min_conf * 100))
with open(fp_fname, "w") as fout:
for sid in e.fp:
def set_taxonomy(self, taxonomy_fname):
self.taxonomy = GGTaxonomyFile(taxonomy_fname)
