# 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
#!/usr/bin/env python

################################################################
### Jose A Espinosa. CSN/CB-CRG Group. Jan 2016              ###
################################################################
### Script creates BedTools objects from a file containing   ###
### mice feeding behavior and uses tools from pybedtools to  ###
### extract intermeals intervals (complement) and intersect  ###
### them with day and experimental phases.                   ###
### Generates a bed file for each track with the result of   ###
### the above described operations.                          ###
################################################################


base_dir = path.dirname(getcwd())
out_dir = base_dir + "/test/"

mapping_data = mapping.MappingInfo(base_dir + "/sample_data/feeding_behavior/b2g.txt")

int_data = intervals.IntData(base_dir + "/sample_data/feeding_behavior/feedingBehavior_HF_mice.csv", map_dict=mapping_data.correspondence)

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"

# 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

#!/usr/bin/env python

################################################################
### Jose A Espinosa. CSN/CB-CRG Group. Jan 2016              ###
################################################################
### Script creates BedTools objects from a file containing   ###
### mice feeding behavior and uses tools from pybedtools to  ###
### extract intermeals intervals (complement) and intersect  ###
### them with day and experimental phases.                   ###
### Generates a bed file for each track with the result of   ###
### the above described operations.                          ###
################################################################


base_dir = path.dirname(getcwd())
out_dir = base_dir + "/test/"

mapping_data = mapping.MappingInfo(base_dir + "/sample_data/feeding_behavior/b2g.txt")

int_data = intervals.IntData(base_dir + "/sample_data/feeding_behavior/feedingBehavior_HF_mice.csv", map_dict=mapping_data.correspondence)

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"