def write_misclassified(self, tax_assign_map, tax_assign_conf, out_fname):
t = self.taxonomy
with open(out_fname, 'w') as fout:
fout.write("; List of misclassified sequences.\n")
fout.write("; Format: 4 lines per sequence\n")
fout.write("; 1 sequence ID\n")
fout.write("; 2 correct assignment\n")
fout.write("; 3 epatax assignment\n")
fout.write("; 4 rank confidence levels\n\n")
for sid in self.miss_list:
fout.write(sid + "\n")
true_ranks = t.get_seq_ranks(sid)
fout.write(Taxonomy.lineage_str(true_ranks) + "\n")
epa_ranks = tax_assign_map[sid]
fout.write(Taxonomy.lineage_str(epa_ranks) + "\n")
rank_conf = tax_assign_conf[sid]
fout.write("\t".join(["%.3f" % conf for conf in rank_conf]) + "\n")
fout.write("\n")
def write_misclassified(self, tax_assign_map, tax_assign_conf, out_fname):
t = self.taxonomy
with open(out_fname, 'w') as fout:
fout.write("; List of misclassified sequences.\n")
fout.write("; Format: 4 lines per sequence\n")
fout.write("; 1 sequence ID\n")
fout.write("; 2 correct assignment\n")
fout.write("; 3 epatax assignment\n")
fout.write("; 4 rank confidence levels\n\n")
for sid in self.miss_list:
fout.write(sid + "\n")
true_ranks = t.get_seq_ranks(sid)
fout.write(Taxonomy.lineage_str(true_ranks) + "\n")
epa_ranks = tax_assign_map[sid]
fout.write(Taxonomy.lineage_str(epa_ranks) + "\n")
rank_conf = tax_assign_conf[sid]
fout.write("\t".join(["%.3f" % conf
for conf in rank_conf]) + "\n")
fout.write("\n")
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:
ranks = mislabel_map[sid]["ranks"]
lvl = mislabel_map[sid]["mis_rank"]
true_ranks = e.taxonomy.get_seq_ranks(sid)
fout.write("%s\t%s\t%s\t%s\n" %
(sid, lvl, Taxonomy.lineage_str(true_ranks),
Taxonomy.lineage_str(ranks)))
tp_fname = os.path.join(out_path,
out_stem + ".eval%d.tp" % int(args.min_conf * 100))
with open(tp_fname, "w") as fout:
for sid in e.tp:
ranks = mislabel_map[sid]["ranks"]
fout.write("%s\t%s\n" % (sid, Taxonomy.lineage_str(ranks)))
fn_fname = os.path.join(out_path,
out_stem + ".eval%d.fn" % int(args.min_conf * 100))
with open(fn_fname, "w") as fout:
for sid in e.fn:
true_ranks = true_taxonomy.get_seq_ranks(sid)
ranks = e.taxonomy.get_seq_ranks(sid)
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:
ranks = mislabel_map[sid]["ranks"]
lvl = mislabel_map[sid]["mis_rank"]
true_ranks = e.taxonomy.get_seq_ranks(sid)
fout.write("%s\t%s\t%s\t%s\n" % (sid, lvl, Taxonomy.lineage_str(true_ranks), Taxonomy.lineage_str(ranks)))
tp_fname = os.path.join(out_path, out_stem + ".eval%d.tp" % int(args.min_conf * 100))
with open(tp_fname, "w") as fout:
for sid in e.tp:
ranks = mislabel_map[sid]["ranks"]
fout.write("%s\t%s\n" % (sid, Taxonomy.lineage_str(ranks)))
fn_fname = os.path.join(out_path, out_stem + ".eval%d.fn" % int(args.min_conf * 100))
with open(fn_fname, "w") as fout:
for sid in e.fn:
true_ranks = true_taxonomy.get_seq_ranks(sid)
ranks = e.taxonomy.get_seq_ranks(sid)
fout.write("%s\t%s\t%s\n" % (sid, Taxonomy.lineage_str(true_ranks), Taxonomy.lineage_str(ranks)))
full_fname = os.path.join(out_path, out_stem + ".eval%d.full" % int(args.min_conf * 100))