# Path: tools/templates.py

# 
# Path: tools/experiment_parser.py
# def parse_all(path, file_filter, err=False, legacy=False):
#     # path = args.path
#     # files = sorted(glob.glob(os.path.join(path, args.filter)))
#     files = sorted(glob.glob(os.path.join(path, file_filter)))
#     # err = not args.no_error
# 
#     table_lines = defaultdict(dict)
#     sequences = set()
# 
#     for fname in files:
#         try:
#             seq_name, cov, error, k, ext, ef = parse_fname(fname, err)
#             repeats = ext[-1] == 'r'
#             sequences.add(seq_name)
#             key = (seq_name, cov, error, k, repeats)
# 
#             table_lines[key]['provided_coverage'] = cov
#             table_lines[key]['provided_error_rate'] = error
#             table_lines[key]['provided_k'] = k
#             table_lines[key]['repeats'] = repeats
#             table_lines[key]['fname'] = fname
#             table_lines[key]['seq_name'] = seq_name
# 
#             if ext == '.est' or ext == '.est_r':
#                 d = parse_estimate(fname)
#                 table_lines[key]['coverage'] = d.get(
#                     'coverage', None)
#                 table_lines[key]['error_rate'] = d.get(
#                     'error_rate', None)
#                 table_lines[key]['loglikelihood'] = d.get(
#                     'loglikelihood', None)
#                 table_lines[key]['q1'] = d.get('q1', None)
#                 table_lines[key]['q2'] = d.get('q2', None)
#                 table_lines[key]['q'] = d.get('q', None)
#                 table_lines[key]['guessed_coverage'] = d.get('guessed_coverage', None)
#                 table_lines[key]['guessed_error_rate'] = d.get('guessed_error_rate', None)
#                 table_lines[key]['guessed_loglikelihood'] = d.get(
#                     'guessed_loglikelihood', None)
#                 table_lines[key]['original_loglikelihood'] = d.get(
#                     'original_loglikelihood', None)
#                 table_lines[key]['genome_size'] = d.get(
#                     'genome_size', None)
#             elif ext == '.fit':
#                 table_lines[key]['williams_genome_size'] = parse_williams(fname)
#             else:
#                 table_lines[key]['khmer_coverage'] = kmer_to_read_coverage(
#                     parse_khmer(fname), k)
#         except Exception as e:
#             print('Unable to process {}\n{}'.format(fname, e), file=sys.stderr)
#     return table_lines
# 
# Path: tools/table_generator.py
# def format_table(header, titles, lines, template_file, escape=None, round_floats=4, is_list=False):
#     def format_val(val):
#         if round_floats and type(val) is float:
#             val = round(val, round_floats)
#         if escape:
#             try:
#                 return escape(val)
#             except:
#                 pass
#         return val
# 
#     if not is_list:
#         lines = lines_to_list(header, lines)
#     data = {
#         'header': [
#             {'value': format_val(titles.get(h, h)), 'first': i == 0, 'last': i == len(header) - 1}
#             for i, h in enumerate(header)
#         ],
#         'body': [
#             {'line': [
#                 {'value': format_val(v), 'first': i == 0, 'last': i == len(l) - 1}
#                 for i, v in enumerate(l)
#             ]} for l in lines
#         ],
#     }
# 
#     with open(template_file) as f:
#         template = f.read()
#         return pystache.render(template, data)


import argparse
from collections import defaultdict
from tools import templates
from tools.experiment_parser import parse_all
from tools.table_generator import format_table
                table_sum[key[1:]][k] += v
                table_cnt[key[1:]][k] += 1.0
            except TypeError:
                pass

    for key, val in table_sum.items():
        for k, v in val.items():
            if table_cnt[key][k] == 0:
                table_avg[key][k] = None
            else:
                table_avg[key][k] = v / table_cnt[key][k]

    for key, val in table_lines.items():
        for k, v in val.items():
            try:
                table_std_sum[key[1:]][k] += (v - table_avg[key[1:]][k]) ** 2
            except TypeError:
                pass

    for key, val in table_std_sum.items():
        for k, v in val.items():
            if table_cnt[key][k] <= 1:
                table_avg[key][k + std_key_suffix] = 0
            else:
                table_avg[key][k + std_key_suffix] = (v / (table_cnt[key][k] - 1)) ** 0.5

    return table_avg


def main(args):

# Path: tools/templates.py

# 
# Path: tools/experiment_parser.py
# def parse_all(path, file_filter, err=False, legacy=False):
#     # path = args.path
#     # files = sorted(glob.glob(os.path.join(path, args.filter)))
#     files = sorted(glob.glob(os.path.join(path, file_filter)))
#     # err = not args.no_error
# 
#     table_lines = defaultdict(dict)
#     sequences = set()
# 
#     for fname in files:
#         try:
#             seq_name, cov, error, k, ext, ef = parse_fname(fname, err)
#             repeats = ext[-1] == 'r'
#             sequences.add(seq_name)
#             key = (seq_name, cov, error, k, repeats)
# 
#             table_lines[key]['provided_coverage'] = cov
#             table_lines[key]['provided_error_rate'] = error
#             table_lines[key]['provided_k'] = k
#             table_lines[key]['repeats'] = repeats
#             table_lines[key]['fname'] = fname
#             table_lines[key]['seq_name'] = seq_name
# 
#             if ext == '.est' or ext == '.est_r':
#                 d = parse_estimate(fname)
#                 table_lines[key]['coverage'] = d.get(
#                     'coverage', None)
#                 table_lines[key]['error_rate'] = d.get(
#                     'error_rate', None)
#                 table_lines[key]['loglikelihood'] = d.get(
#                     'loglikelihood', None)
#                 table_lines[key]['q1'] = d.get('q1', None)
#                 table_lines[key]['q2'] = d.get('q2', None)
#                 table_lines[key]['q'] = d.get('q', None)
#                 table_lines[key]['guessed_coverage'] = d.get('guessed_coverage', None)
#                 table_lines[key]['guessed_error_rate'] = d.get('guessed_error_rate', None)
#                 table_lines[key]['guessed_loglikelihood'] = d.get(
#                     'guessed_loglikelihood', None)
#                 table_lines[key]['original_loglikelihood'] = d.get(
#                     'original_loglikelihood', None)
#                 table_lines[key]['genome_size'] = d.get(
#                     'genome_size', None)
#             elif ext == '.fit':
#                 table_lines[key]['williams_genome_size'] = parse_williams(fname)
#             else:
#                 table_lines[key]['khmer_coverage'] = kmer_to_read_coverage(
#                     parse_khmer(fname), k)
#         except Exception as e:
#             print('Unable to process {}\n{}'.format(fname, e), file=sys.stderr)
#     return table_lines
# 
# Path: tools/table_generator.py
# def format_table(header, titles, lines, template_file, escape=None, round_floats=4, is_list=False):
#     def format_val(val):
#         if round_floats and type(val) is float:
#             val = round(val, round_floats)
#         if escape:
#             try:
#                 return escape(val)
#             except:
#                 pass
#         return val
# 
#     if not is_list:
#         lines = lines_to_list(header, lines)
#     data = {
#         'header': [
#             {'value': format_val(titles.get(h, h)), 'first': i == 0, 'last': i == len(header) - 1}
#             for i, h in enumerate(header)
#         ],
#         'body': [
#             {'line': [
#                 {'value': format_val(v), 'first': i == 0, 'last': i == len(l) - 1}
#                 for i, v in enumerate(l)
#             ]} for l in lines
#         ],
#     }
# 
#     with open(template_file) as f:
#         template = f.read()
#         return pystache.render(template, data)


# Path: tools/experiment_table.py
import argparse
from collections import defaultdict
from tools import templates
from tools.experiment_parser import parse_all
from tools.table_generator import format_table

                table_sum[key[1:]][k] += v
                table_cnt[key[1:]][k] += 1.0
            except TypeError:
                pass

    for key, val in table_sum.items():
        for k, v in val.items():
            if table_cnt[key][k] == 0:
                table_avg[key][k] = None
            else:
                table_avg[key][k] = v / table_cnt[key][k]

    for key, val in table_lines.items():
        for k, v in val.items():
            try:
                table_std_sum[key[1:]][k] += (v - table_avg[key[1:]][k]) ** 2
            except TypeError:
                pass

    for key, val in table_std_sum.items():
        for k, v in val.items():
            if table_cnt[key][k] <= 1:
                table_avg[key][k + std_key_suffix] = 0
            else:
                table_avg[key][k + std_key_suffix] = (v / (table_cnt[key][k] - 1)) ** 0.5

    return table_avg


def main(args):

    table_lines = parse_all(args.path, args.filter, not args.no_error, legacy=args.legacy)