fig, ax = plt.subplots(figsize=(10, 6)) patches = [] f_color_v = [] e_color_v = [] lw_v = [] paths, segSeqD, circular_D = vu.parse_cycles_file(args.cycles_file) path_num = args.path path = paths[path_num] if args.reduce_path != [0, 0]: isCycle = False else: isCycle = circular_D[path_num] prev_seg_index_is_adj = vu.adjacent_segs(path, segSeqD, isCycle) print("PSIIA", prev_seg_index_is_adj) raw_path_length = vu.get_raw_path_length(path, segSeqD) bpg_dict, seg_end_pos_d = {}, {} if args.graph: bpg_dict, seg_end_pos_d = vu.parse_BPG(args.graph) gene_set = set() if args.gene_subset_file.upper() == "BUSHMAN": sourceDir = os.path.dirname(os.path.abspath(__file__)) args.gene_subset_file = sourceDir + "/resources/Bushman_group_allOnco_May2018.tsv" if args.gene_subset_file: gff = True if args.gene_subset_file.endswith(".gff") else False
gene_tree = vu.parse_genes(args.ref) print("Unaligned fraction cutoff set to " + str(vu.unaligned_cutoff_frac)) chromosome_colors = vu.get_chr_colors() plt.clf() fig, ax = plt.subplots() patches = [] f_color_v = [] e_color_v = [] lw_v = [] cycles, segSeqD, circular_D = vu.parse_cycles_file(args.cycles_file) cycle_num = args.cycle isCycle = circular_D[cycle_num] cycle = cycles[cycle_num] prev_seg_index_is_adj = vu.adjacent_segs(cycle, segSeqD, isCycle) raw_cycle_length = vu.get_raw_path_length(cycle, segSeqD) gene_fontsize = args.gene_fontsize tick_fontsize = args.tick_fontsize bpg_dict, seg_end_pos_d = {}, {} if args.graph: bpg_dict, seg_end_pos_d = vu.parse_BPG(args.graph) gene_set = set() if args.gene_subset_file.upper() == "BUSHMAN": sourceDir = os.path.dirname(os.path.abspath(__file__)) args.gene_subset_file = sourceDir + "/Bushman_group_allOnco_May2018.tsv"