def plot_BAF_heatmap(args): if PLT_AVAIL == True: pass else: print "matplotlib.pyplot not available, skip plotting..." sys.stdout.flush() sys.exit(-1) BAF_heatmap = BAFHeatMap() BAF_heatmap.read_heatmap(args.filename_base) BAF_heatmap.get_color_max() segments = Segments() inseg_file_name = args.filename_base + ".PyLOH.segments" segments.read_segfile(inseg_file_name) seg_num = segments.num outheatmap_dir_name = args.filename_base + ".PyLOH.heatmap.plot" if os.path.exists(outheatmap_dir_name) == False: os.mkdir(outheatmap_dir_name) for j in range(0, seg_num): BAF_counts_j = BAF_heatmap.BAF_counts[j] seg_name_j = segments[j][0] print "Plotting segment {0}...".format(seg_name_j) sys.stdout.flush() plot_BAF_heatmap_by_segment(BAF_counts_j, seg_name_j, outheatmap_dir_name)
def plot_BAF_heatmap(args): if PLT_AVAIL == True: pass else: print "matplotlib.pyplot not available, skip plotting..." sys.stdout.flush() sys.exit(-1) BAF_heatmap = BAFHeatMap() BAF_heatmap.read_heatmap(args.filename_base) BAF_heatmap.get_color_max() segments = Segments() inseg_file_name = args.filename_base + '.PyLOH.segments' segments.read_segfile(inseg_file_name) seg_num = segments.num outheatmap_dir_name = args.filename_base + '.PyLOH.heatmap.plot' if os.path.exists(outheatmap_dir_name) == False: os.mkdir(outheatmap_dir_name) for j in range(0, seg_num): BAF_counts_j = BAF_heatmap.BAF_counts[j] seg_name_j = segments[j][0] print 'Plotting segment {0}...'.format(seg_name_j) sys.stdout.flush() plot_BAF_heatmap_by_segment(BAF_counts_j, seg_name_j, outheatmap_dir_name)
def run_preprocess(args): normal_bam = pysam.Samfile(args.normal_bam, 'rb') tumor_bam = pysam.Samfile(args.tumor_bam, 'rb') segments = Segments() if args.segments_bed == None: print 'Loading segments by 22 autosomes...' sys.stdout.flush() segments.segmentation_by_chrom(normal_bam, tumor_bam) else: print 'Loading segments by {0}...'.format(args.segments_bed) sys.stdout.flush() segments.segmentation_by_bed(normal_bam, tumor_bam, args.segments_bed) normal_bam.close() tumor_bam.close() time_start = time.time() converter = BamToDataConverter( args.normal_bam, args.tumor_bam, args.reference_genome, args.filename_base, segments, WES_flag=args.WES, min_depth=args.min_depth, min_bqual=args.min_base_qual, min_mqual=args.min_map_qual, process_num = args.process_num ) converter.convert() time_end = time.time() print 'Run time: {0:.2f} seconds'.format(time_end - time_start) sys.stdout.flush()