# Path: covest/constants.py
# DEFAULT_K = 21
# 
# Path: covest/data.py
# def sample_reads(src_reads_file, dest_reads_file, factor):
#     prob = 1.0 / factor
#     with open(dest_reads_file, 'w') as f:
#         for read_id, read in load_reads(src_reads_file):
#             if random.random() < prob:
#                 f.write('>{}\n'.format(read_id))
#                 f.write('{}\n'.format(read))
# 
# 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: covest/utils.py
# def run(command, shell=False, output=None, verbose=False):
#     if verbose:
#         print(command, file=sys.stderr)
#     f = open(output, 'w') if output else None
#     if not shell:
#         command = command.split()
#     return subprocess.call(command, shell=shell, stdout=f)


import argparse
import json
import os
import shutil
import sys
from pathlib import Path
from tempfile import mkstemp
from covest.constants import DEFAULT_K
from covest.data import sample_reads as _sample_reads, count_reads_stats
from covest.utils import run
    except Exception as e:
        config = dict()
        if src_config_file is not None:
            print(src_config_file, e, file=sys.stderr)
    config['reads'] = str(reads_file.name)
    return config


def calculate_reads_stats(reads_file, config, reads_info=None):
    if reads_info:
        read_length, reads_size = reads_info
    else:
        print('Calculating read length and size...', file=sys.stderr)
        read_length, reads_size = count_reads_stats(str(reads_file))
        print('read length: %d, size: %d' % (read_length, reads_size), file=sys.stderr)

    config.update({
        'reads_size': reads_size,
        'r': read_length,
    })
    return config


def generate_histogram(reads_file, dest_dir, config, clean=False):
    print('Generating histogram...', file=sys.stderr)
    hist_file = dest_dir / HISTOGRAM_FILENAME
    jellyfish_count = 'jellyfish count -m {k} -s 500M -t 16 -C {infile} -o {infile}.jf'
    jellyfish_hist = 'jellyfish histo {infile}.jf -o {outfile}'

    params = {

# Path: covest/constants.py
# DEFAULT_K = 21
# 
# Path: covest/data.py
# def sample_reads(src_reads_file, dest_reads_file, factor):
#     prob = 1.0 / factor
#     with open(dest_reads_file, 'w') as f:
#         for read_id, read in load_reads(src_reads_file):
#             if random.random() < prob:
#                 f.write('>{}\n'.format(read_id))
#                 f.write('{}\n'.format(read))
# 
# 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: covest/utils.py
# def run(command, shell=False, output=None, verbose=False):
#     if verbose:
#         print(command, file=sys.stderr)
#     f = open(output, 'w') if output else None
#     if not shell:
#         command = command.split()
#     return subprocess.call(command, shell=shell, stdout=f)


# Path: tools/prepare_experiment.py
import argparse
import json
import os
import shutil
import sys
from pathlib import Path
from tempfile import mkstemp
from covest.constants import DEFAULT_K
from covest.data import sample_reads as _sample_reads, count_reads_stats
from covest.utils import run

    except Exception as e:
        config = dict()
        if src_config_file is not None:
            print(src_config_file, e, file=sys.stderr)
    config['reads'] = str(reads_file.name)
    return config


def calculate_reads_stats(reads_file, config, reads_info=None):
    if reads_info:
        read_length, reads_size = reads_info
    else:
        print('Calculating read length and size...', file=sys.stderr)
        read_length, reads_size = count_reads_stats(str(reads_file))
        print('read length: %d, size: %d' % (read_length, reads_size), file=sys.stderr)

    config.update({
        'reads_size': reads_size,
        'r': read_length,
    })
    return config


def generate_histogram(reads_file, dest_dir, config, clean=False):
    print('Generating histogram...', file=sys.stderr)
    hist_file = dest_dir / HISTOGRAM_FILENAME
    jellyfish_count = 'jellyfish count -m {k} -s 500M -t 16 -C {infile} -o {infile}.jf'
    jellyfish_hist = 'jellyfish histo {infile}.jf -o {outfile}'

    params = {

        'k': DEFAULT_K,