for f in args.file_mice_behavior:
int_data = intervals.IntData(f, map_dict=mapping_data.correspondence)
data_read = int_data.read(relative_coord=True)
chr_file_n = "chrom"
mapping.write_chr_sizes(data_read, file_n=chr_file_n)
chr_file = chr_file_n + ".sizes"
if end_time < int_data.max - int_data.min:
end_time = int_data.max - int_data.min
if not data_read_all_batches:
data_read_all_batches = data_read
else:
data_read_all_batches = tracks.merge_tracks(data_read_all_batches,
data_read)
stdout.write(str(end_time))
list_ctrl = [1, 3, 5, 7, 9, 11, 13, 15, 17]
list_hf = [2, 4, 8, 10, 12, 14, 16, 18]
bed_dict = dict()
bed_dict['ctrl'] = {}
bed_dict['hf'] = {}
bed_dict['ctrl']['food'] = data_read_all_batches.convert(
mode="bed",
data_types=data_type_joined,
data_types_actions="all",
makedirs(out_dir)
chdir(out_dir)
data_read_b1 = int_data_b1.read(relative_coord=True)
data_read_b2 = int_data_b2.read(relative_coord=True)
data_read_b3 = int_data_b3.read(relative_coord=True)
data_read_b4 = int_data_b4.read(relative_coord=True)
# Check the longest period of time of any batches
end_time = max (int_data_b1.max - int_data_b1.min,
int_data_b2.max - int_data_b2.min,
int_data_b3.max - int_data_b3.min,
int_data_b4.max - int_data_b4.min)
data_read_all_batches = tracks.merge_tracks (tracks.merge_tracks (tracks.merge_tracks (data_read_b1, data_read_b2), data_read_b3), data_read_b4)
list_wt_sal = [1,3,5,13,15,17,25,27,29,37,39,41]
list_wt_nic = [7,9,11,19,21,23,31,33,35,43,45,47]
list_KO_cb1_sal = [6,8,10,18,20,22,30,32,34,42,44,46]
list_KO_cb1_nic = [2,4,12,14,16,24,26,28,36,38,40,48]
bed_dict = dict()
bed_dict ['wt_saline'] = {}
bed_dict ['wt_nicotine'] = {}
bed_dict ['KO_cb1_saline'] = {}
bed_dict ['KO_cb1_nicotine'] = {}
bed_dict ['wt_saline'][data_type_1] = data_read_all_batches.convert(mode="bed", data_types=[data_type_1],
color_restrictions=data_type_col, tracks=list_wt_sal)
makedirs(out_dir)
chdir(out_dir)
data_read_b1 = int_data_b1.read(relative_coord=True)
data_read_b2 = int_data_b2.read(relative_coord=True)
data_read_b3 = int_data_b3.read(relative_coord=True)
data_read_b4 = int_data_b4.read(relative_coord=True)
# Check the longest period of time of any batches
end_time = max(int_data_b1.max - int_data_b1.min,
int_data_b2.max - int_data_b2.min,
int_data_b3.max - int_data_b3.min,
int_data_b4.max - int_data_b4.min)
data_read_all_batches = tracks.merge_tracks(
tracks.merge_tracks(tracks.merge_tracks(data_read_b1, data_read_b2),
data_read_b3), data_read_b4)
list_wt = [item for item in data_read_all_batches.list_tracks if int(item) % 2]
list_KO_cb1 = [
item for item in data_read_all_batches.list_tracks if not int(item) % 2
]
data_type_col = {data_type_1: 'orange', data_type_1: 'black'}
bed_dict = dict()
bed_dict['wt'] = {}
bed_dict['KO_cb1'] = {}
bed_dict['wt'][data_type_1] = data_read_all_batches.convert(