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(