# 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):


from argparse import ArgumentParser
from os       import path, getcwd
from csv      import writer
from pergola  import mapping
from pergola  import intervals
from sys      import stderr, exit
import pybedtools
parser.add_argument('-t', '--tag_out', required=False, type=str, help='Tag output file')

args = parser.parse_args()

if args.tag_out:
    tag_file = args.tag_out
else:
    tag_file = "mean_speed_i_motionDir"

print >> stderr, "Bed speed file: %s" % args.phenotypic_file
print >> stderr, "Bed motion file: %s" % args.motion_file
print >> stderr, "Mapping bed to Pergola file: %s" % args.bed_mapping_file
print >> stderr, "Output tag file: %s" % tag_file

mapping_bed = mapping.MappingInfo(args.bed_mapping_file)
## mapping_bed = mapping.MappingInfo("/Users/jespinosa/git/pergola/test/c_elegans_data_test/bed2pergola.txt")

bed_ph_file = args.phenotypic_file

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

phenotypic_data_read = int_data_phenotypic.read(relative_coord=False)
bed_obj_phenotypic = phenotypic_data_read.convert(mode="bed")
key_s = bed_obj_phenotypic.keys()[0]
phenotypic_feature_bt = bed_obj_phenotypic[key_s].create_pybedtools()

###################
# Generate two BedTool objects containing motion type (forward, backward, paused)
motion_bed_file = args.motion_file

# 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: examples/N2_vs_case_strain_distros/bin/celegans_feature_i_motion.py
from argparse import ArgumentParser
from os       import path, getcwd
from csv      import writer
from pergola  import mapping
from pergola  import intervals
from sys      import stderr, exit
import pybedtools

parser.add_argument('-t', '--tag_out', required=False, type=str, help='Tag output file')

args = parser.parse_args()

if args.tag_out:
    tag_file = args.tag_out
else:
    tag_file = "mean_speed_i_motionDir"

print >> stderr, "Bed speed file: %s" % args.phenotypic_file
print >> stderr, "Bed motion file: %s" % args.motion_file
print >> stderr, "Mapping bed to Pergola file: %s" % args.bed_mapping_file
print >> stderr, "Output tag file: %s" % tag_file

mapping_bed = mapping.MappingInfo(args.bed_mapping_file)
## mapping_bed = mapping.MappingInfo("/Users/jespinosa/git/pergola/test/c_elegans_data_test/bed2pergola.txt")

bed_ph_file = args.phenotypic_file

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

phenotypic_data_read = int_data_phenotypic.read(relative_coord=False)
bed_obj_phenotypic = phenotypic_data_read.convert(mode="bed")
key_s = bed_obj_phenotypic.keys()[0]
phenotypic_feature_bt = bed_obj_phenotypic[key_s].create_pybedtools()

###################
# Generate two BedTool objects containing motion type (forward, backward, paused)
motion_bed_file = args.motion_file

int_data_motion = intervals.IntData(motion_bed_file, map_dict=mapping_bed.correspondence, header=False, 