# 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


def comp_with_value(f):
    """
    adds 10 bp to the stop
    """
    score = int(f[2]) - int(f[1])
    return (f, score)


def gen(bed_comp):
    for i in bed_comp:
        score = int(i[2])-int(i[1])
        new_i = (i[0], i[1], i[2], ".", score) 
        
        yield new_i

def reorder(bed_comp_phases):
    for i in bed_comp_phases:        
        new_i = (i[0], i[1], i[2], i[5]) 
        
        yield new_i
                
# For each track merge feeding acts that are separated by less than 120 seconds (thus generating feeding bouts track)
# Calculates the complement of feeding bouts (intermeal intervals) and intersect them with day and experimental phases
# Dumping results into bed files
for tr, bed in bed_str.iteritems():
    bed_BedTools = bed.create_pybedtools()
    bed_merged_fn = bed_BedTools.merge(d=120, stream=True, c=(4,5,6,9), o=("distinct","sum","distinct","collapse")).saveas().fn
    

# 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



def comp_with_value(f):
    """
    adds 10 bp to the stop
    """
    score = int(f[2]) - int(f[1])
    return (f, score)


def gen(bed_comp):
    for i in bed_comp:
        score = int(i[2])-int(i[1])
        new_i = (i[0], i[1], i[2], ".", score) 
        
        yield new_i

def reorder(bed_comp_phases):
    for i in bed_comp_phases:        
        new_i = (i[0], i[1], i[2], i[5]) 
        
        yield new_i
                
# For each track merge feeding acts that are separated by less than 120 seconds (thus generating feeding bouts track)
# Calculates the complement of feeding bouts (intermeal intervals) and intersect them with day and experimental phases
# Dumping results into bed files
for tr, bed in bed_str.iteritems():
    bed_BedTools = bed.create_pybedtools()
    bed_merged_fn = bed_BedTools.merge(d=120, stream=True, c=(4,5,6,9), o=("distinct","sum","distinct","collapse")).saveas().fn
    

    pybed_intdata = intervals.IntData(bed_merged_fn, map_dict=mapping_bed.correspondence, header=False, fields_names=['chrm', 'start', 'end', 'nature', 'value', 'strain', 'color'])