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_set = vu.parse_gene_subset_file(args.gene_subset_file, gff)
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,isCycle,prev_seg_index_is_adj) 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: gene_set = vu.parse_gene_subset_file(args.gene_subset_file) # for i,k in seg_end_pos_d.iteritems(): # print i,k # print "" # for i,k in bpg_dict.iteritems(): # print i,k
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" if args.gene_subset_file and not args.gene_subset_file == "NO":
path = paths[path_num] if args.reduce_path != [0, 0]: isCycle = False else: isCycle = circular_D[path_num] #debug # vu.reduce_path(path,) # print "PATH:",path # print "SEGSEQD",segSeqD prev_seg_index_is_adj = vu.adjacent_segs(path, segSeqD, isCycle) print path print "PSIIA", prev_seg_index_is_adj raw_path_length = vu.get_raw_path_length(path, segSeqD, False, prev_seg_index_is_adj) 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: gene_set = vu.parse_gene_subset_file(args.gene_subset_file) elif args.gene_subset_list: gene_set = set(args.gene_subset_list) if not args.om_alignments: ref_placements, total_length = construct_path_ref_placements( path, segSeqD, raw_path_length, prev_seg_index_is_adj)