# 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: pergola/tracks.py
# class GenomicContainer(object):
# class Track(GenomicContainer):
# class BedToolConvertible(GenomicContainer):
# class Bed(BedToolConvertible):
# class BedGraph(BedToolConvertible):
# class Gff(BedToolConvertible):
#     def __init__(self, data, fields=None, data_types=None, **kwargs):
#     def __iter__(self):
#     def next(self):
#     def save_track(self, mode="w", path=None, name_file=None, track_line=True, bed_label=False, gff_label=False):
#     def __init__(self, data, fields=None, data_types=None, list_tracks=None, min=0, max=0, **kwargs):
#     def convert(self, mode='bed', range_color=None, **kwargs):
#     def _convert2single_track(self, data_tuples,  mode=None, **kwargs):
#     def _get_range(self, data_tr):
#     def remove(self, dict_t, tracks2remove):
#     def join_by_track(self, dict_t, tracks2join):  
#     def join_by_dataType (self, dict_d, mode):
#     def track_convert2bed(self, track, in_call=False, **kwargs):
#     def track_convert2gff(self, track, in_call=False, **kwargs):
#     def track_convert2bedGraph(self, track, in_call=False, window=300, mean_win=False, mean_value=False,  **kwargs):
#     def __init__(self, data, **kwargs):
#     def create_pybedtools(self):
#     def _tmp_track(self):
#     def __init__(self, data, **kwargs):
#     def __init__(self, data, **kwargs):
#     def win_mean (self):
#     def _win_mean (self, data, n_tracks):     
#     def __init__(self, data, **kwargs):
# def assign_color(set_data_types, color_restrictions=None):
# def merge_tracks (tr_1, tr_2):


from pergola import mapping, intervals, tracks
from os import path, getcwd
#!/usr/bin/env python

################################################################
### Jose A Espinosa. CSN/CB-CRG Group. Jan 2016              ###
################################################################
###    ###
###   ###
###   ###
###                    ###
###    ###
###                           ###
################################################################


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

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


# 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: pergola/tracks.py
# class GenomicContainer(object):
# class Track(GenomicContainer):
# class BedToolConvertible(GenomicContainer):
# class Bed(BedToolConvertible):
# class BedGraph(BedToolConvertible):
# class Gff(BedToolConvertible):
#     def __init__(self, data, fields=None, data_types=None, **kwargs):
#     def __iter__(self):
#     def next(self):
#     def save_track(self, mode="w", path=None, name_file=None, track_line=True, bed_label=False, gff_label=False):
#     def __init__(self, data, fields=None, data_types=None, list_tracks=None, min=0, max=0, **kwargs):
#     def convert(self, mode='bed', range_color=None, **kwargs):
#     def _convert2single_track(self, data_tuples,  mode=None, **kwargs):
#     def _get_range(self, data_tr):
#     def remove(self, dict_t, tracks2remove):
#     def join_by_track(self, dict_t, tracks2join):  
#     def join_by_dataType (self, dict_d, mode):
#     def track_convert2bed(self, track, in_call=False, **kwargs):
#     def track_convert2gff(self, track, in_call=False, **kwargs):
#     def track_convert2bedGraph(self, track, in_call=False, window=300, mean_win=False, mean_value=False,  **kwargs):
#     def __init__(self, data, **kwargs):
#     def create_pybedtools(self):
#     def _tmp_track(self):
#     def __init__(self, data, **kwargs):
#     def __init__(self, data, **kwargs):
#     def win_mean (self):
#     def _win_mean (self, data, n_tracks):     
#     def __init__(self, data, **kwargs):
# def assign_color(set_data_types, color_restrictions=None):
# def merge_tracks (tr_1, tr_2):


# Path: test/gff_creation_test.py
from pergola import mapping, intervals, tracks
from os import path, getcwd

#!/usr/bin/env python

################################################################
### Jose A Espinosa. CSN/CB-CRG Group. Jan 2016              ###
################################################################
###    ###
###   ###
###   ###
###                    ###
###    ###
###                           ###
################################################################


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)