# 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/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):


import pybedtools
from os import path, getcwd
from pergola import mapping
from pergola import intervals

data_read = int_data.read(relative_coord=True)

###################
# Generate to BedTool objects containing light and dark phases
# Write phases file
total_time = int_data.max - int_data.min
mapping.write_cytoband(end = total_time, delta=43200, start_phase="dark")
light_ph_f = out_dir +  "phases_light.bed"
dark_ph_f = out_dir + "phases_dark.bed"
all_phases = out_dir + "phases.bed"

light_bed = pybedtools.BedTool(light_ph_f)
dark_bed = pybedtools.BedTool(dark_ph_f)
all_phases_bed = pybedtools.BedTool(all_phases)

# Generate a chr.size file in order to calculate complement of merged meals
chr_file_n = "chrom"
mapping.write_chr_sizes (data_read, path_w=out_dir, file_n=chr_file_n)
chr_file = out_dir + chr_file_n + ".sizes"

# Dictionary to set colors of each type of food
data_type_col = {'food_sc': 'orange', 'food_fat':'blue'}

bed_str = data_read.convert(mode="bed", data_types=["food_sc", "food_fat"], data_types_actions="all", color_restrictions=data_type_col)
mapping_bed = mapping.MappingInfo(out_dir + "/pybed2perg.txt")

# Experimentals phases
# Habituation phase (before high-fat food introduction)
# Development phase (after high-fat food introduction)

# 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/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: test/pybed_pergola_newFunction.py
import pybedtools
from os import path, getcwd
from pergola import mapping
from pergola import intervals


data_read = int_data.read(relative_coord=True)

###################
# Generate to BedTool objects containing light and dark phases
# Write phases file
total_time = int_data.max - int_data.min
mapping.write_cytoband(end = total_time, delta=43200, start_phase="dark")
light_ph_f = out_dir +  "phases_light.bed"
dark_ph_f = out_dir + "phases_dark.bed"
all_phases = out_dir + "phases.bed"

light_bed = pybedtools.BedTool(light_ph_f)
dark_bed = pybedtools.BedTool(dark_ph_f)
all_phases_bed = pybedtools.BedTool(all_phases)

# Generate a chr.size file in order to calculate complement of merged meals
chr_file_n = "chrom"
mapping.write_chr_sizes (data_read, path_w=out_dir, file_n=chr_file_n)
chr_file = out_dir + chr_file_n + ".sizes"

# Dictionary to set colors of each type of food
data_type_col = {'food_sc': 'orange', 'food_fat':'blue'}

bed_str = data_read.convert(mode="bed", data_types=["food_sc", "food_fat"], data_types_actions="all", color_restrictions=data_type_col)
mapping_bed = mapping.MappingInfo(out_dir + "/pybed2perg.txt")

# Experimentals phases
# Habituation phase (before high-fat food introduction)
# Development phase (after high-fat food introduction)

mapping_file_data_exp_ph = mapping.MappingInfo(base_dir + "/sample_data/feeding_behavior/f2g.txt")