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()
