# Path: pergola/intervals.py
# class IntData(object):
#     def __init__(self, path, map_dict, header=True, **kwargs):
#     def _check_delimiter (self, path, delimiter):
#     def _reader_data(self):
#     def _pandas_df_reader(self, df):
#     def _set_fields_b(self, fields=None):
#     def _set_fields_g (self, map_dict):
#     def _simple_read(self):
#     def get_field_items(self, data, field="data_types", default=None):
#     def read(self, fields=None, relative_coord=False, intervals=False, int_step=None, fields2rel=None, multiply_t=None,
#              **kwargs):
#     def _min_max(self, list_data, f_start="start", f_end="end"):
#     def _time2rel_time(self, i_fields):
#     def _multiply_values(self, i_fields, factor=1):
#     def _create_int(self, start_int, int_step=None):
#     def _create_int_add_integ(self, start_int, integer=1):
#     def __del__(self):
# def is_number(var):
# def num(s):
# 
# Path: pergola/mapping.py
# class MappingInfo():
#     def __init__(self, path, **kwargs):
#     def _correspondence_from_config(self, path):
#     def _tab_config(self, file_tab):
#     def _mapping_config(self, file_map):
#     def write(self, indent=0):
# def check_path(path):
# def write_chr(self, mode="w", path_w=None, min_c=None, max_c=None):
# def write_chr_sizes(self, mode="w", path_w=None, file_n=None, min_c=None, max_c=None):
# def write_cytoband(end, start=0, delta=43200, start_phase="light", mode="w", path_w=None, lab_bed=True, track_line=True):
# def write_period_seq (end, start=0, delta=43200, tag="day", mode="w", path_w=None, name_file="period_seq", lab_bed=True, track_line=True):
# 
# Path: pergola/parsers.py
# PATH = abspath(split(realpath(__file__))[0])
# def parse_num_range(string):
# def read_track_actions (tracks, track_action = "split_all"):
# def read_colors (path_color_file):


from pergola  import intervals
from pergola  import mapping
from argparse import ArgumentParser
from sys      import stderr, exit
from os.path import basename, splitext
from pergola import parsers
    if window_mean:
        print("@@@Pergola_rules.py: Window mean set to....................... %d" % window_mean, file=stderr)
    else:      
        window_mean = False

    if value_mean:
        print("@@@Pergola_rules.py: Value mean set to....................... %d" % value_mean, file=stderr)
    else:
        value_mean = False

    if no_track_line:
        track_line=False
    else:
        track_line=True
        
    print("@@@Pergola_rules.py: track_line set to............................ %s" % track_line, file=stderr)
    
    # Handling input file field delimiter    
    if not separator:
        separator = "\t"
        print("@@@Pergola_rules.py input file field separator set by default to...... \"\\t\".", file=stderr)
    else:        
        print("@@@Pergola_rules.py input file field separator set to..... \"%s\"" % separator, file=stderr)
    
    if bed_lab_sw:
        bed_lab = True
        print("@@@Pergola_rules.py: bed_label set to......................... %s" % bed_lab, file=stderr)
    else:
        bed_lab = False


# Path: pergola/intervals.py
# class IntData(object):
#     def __init__(self, path, map_dict, header=True, **kwargs):
#     def _check_delimiter (self, path, delimiter):
#     def _reader_data(self):
#     def _pandas_df_reader(self, df):
#     def _set_fields_b(self, fields=None):
#     def _set_fields_g (self, map_dict):
#     def _simple_read(self):
#     def get_field_items(self, data, field="data_types", default=None):
#     def read(self, fields=None, relative_coord=False, intervals=False, int_step=None, fields2rel=None, multiply_t=None,
#              **kwargs):
#     def _min_max(self, list_data, f_start="start", f_end="end"):
#     def _time2rel_time(self, i_fields):
#     def _multiply_values(self, i_fields, factor=1):
#     def _create_int(self, start_int, int_step=None):
#     def _create_int_add_integ(self, start_int, integer=1):
#     def __del__(self):
# def is_number(var):
# def num(s):
# 
# Path: pergola/mapping.py
# class MappingInfo():
#     def __init__(self, path, **kwargs):
#     def _correspondence_from_config(self, path):
#     def _tab_config(self, file_tab):
#     def _mapping_config(self, file_map):
#     def write(self, indent=0):
# def check_path(path):
# def write_chr(self, mode="w", path_w=None, min_c=None, max_c=None):
# def write_chr_sizes(self, mode="w", path_w=None, file_n=None, min_c=None, max_c=None):
# def write_cytoband(end, start=0, delta=43200, start_phase="light", mode="w", path_w=None, lab_bed=True, track_line=True):
# def write_period_seq (end, start=0, delta=43200, tag="day", mode="w", path_w=None, name_file="period_seq", lab_bed=True, track_line=True):
# 
# Path: pergola/parsers.py
# PATH = abspath(split(realpath(__file__))[0])
# def parse_num_range(string):
# def read_track_actions (tracks, track_action = "split_all"):
# def read_colors (path_color_file):


# Path: pergola/scripts/pergola_rules.py
from pergola  import intervals
from pergola  import mapping
from argparse import ArgumentParser
from sys      import stderr, exit
from os.path import basename, splitext
from pergola import parsers

    if window_mean:
        print("@@@Pergola_rules.py: Window mean set to....................... %d" % window_mean, file=stderr)
    else:      
        window_mean = False

    if value_mean:
        print("@@@Pergola_rules.py: Value mean set to....................... %d" % value_mean, file=stderr)
    else:
        value_mean = False

    if no_track_line:
        track_line=False
    else:
        track_line=True
        
    print("@@@Pergola_rules.py: track_line set to............................ %s" % track_line, file=stderr)
    
    # Handling input file field delimiter    
    if not separator:
        separator = "\t"
        print("@@@Pergola_rules.py input file field separator set by default to...... \"\\t\".", file=stderr)
    else:        
        print("@@@Pergola_rules.py input file field separator set to..... \"%s\"" % separator, file=stderr)
    
    if bed_lab_sw:
        bed_lab = True
        print("@@@Pergola_rules.py: bed_label set to......................... %s" % bed_lab, file=stderr)
    else:
        bed_lab = False


    intData = intervals.IntData(path, map_dict=map_file_dict.correspondence,