# Path: covest/data.py
# def count_reads_stats(fname):
#     s = n = 0
#     for _, read in load_reads(fname):
#         s += len(read)
#         n += 1
# 
#     ar = round(s / n) if n else 0
#     return ar, s
# 
# 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 covest.data import count_reads_stats
from tools.experiment_parser import parse_all
from tools.table_generator import format_table
    format_templates = {
        'html': 'templates/html.tpl',
        'csv': 'templates/csv.tpl',
        'tex': 'templates/tex.tpl',
    }

    format_escape = {
        'tex': lambda x: x.replace('_', '\\_'),
    }

    titles = {
        'original_coverage': 'Coverage',
        'original_error_rate': 'Error Rate',
        'estimated_coverage': 'Est. Coverage',
        'estimated_coverage_std': 'Est. Coverage Std',
        'estimated_error_rate': 'Est. Error Rate',
        'estimated_error_rate_std': 'Est. Error Rate Std',
        'estimated_genome_size': 'Est. Genome Size',
        'estimated_genome_size_std': 'Est. Genome Size Std',
    }

    if args.average:
        table_lines = compute_average(table_lines)
        header = [
            'original_coverage', 'original_error_rate',
            'estimated_coverage', 'estimated_coverage_std',
            'estimated_error_rate', 'estimated_error_rate_std',
            'estimated_genome_size', 'estimated_genome_size_std',
        ]


# Path: covest/data.py
# def count_reads_stats(fname):
#     s = n = 0
#     for _, read in load_reads(fname):
#         s += len(read)
#         n += 1
# 
#     ar = round(s / n) if n else 0
#     return ar, s
# 
# 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/williams_table.py
import argparse
from collections import defaultdict
from covest.data import count_reads_stats
from tools.experiment_parser import parse_all
from tools.table_generator import format_table

    format_templates = {
        'html': 'templates/html.tpl',
        'csv': 'templates/csv.tpl',
        'tex': 'templates/tex.tpl',
    }

    format_escape = {
        'tex': lambda x: x.replace('_', '\\_'),
    }

    titles = {
        'original_coverage': 'Coverage',
        'original_error_rate': 'Error Rate',
        'estimated_coverage': 'Est. Coverage',
        'estimated_coverage_std': 'Est. Coverage Std',
        'estimated_error_rate': 'Est. Error Rate',
        'estimated_error_rate_std': 'Est. Error Rate Std',
        'estimated_genome_size': 'Est. Genome Size',
        'estimated_genome_size_std': 'Est. Genome Size Std',
    }

    if args.average:
        table_lines = compute_average(table_lines)
        header = [
            'original_coverage', 'original_error_rate',
            'estimated_coverage', 'estimated_coverage_std',
            'estimated_error_rate', 'estimated_error_rate_std',
            'estimated_genome_size', 'estimated_genome_size_std',
        ]


    print(format_table(