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 convert(self):
seg_num = self.segments.num
process_num = self.process_num
if process_num > seg_num:
process_num = seg_num
pool = Pool(processes = process_num)
args_list = []
for j in range(0, seg_num):
seg_name = self.segments[j][0]
chrom = self.segments[j][1]
start = self.segments[j][2]
end = self.segments[j][3]
args_tuple = (seg_name, chrom, start, end, self.normal_bam_filename,
self.tumor_bam_filename, self.reference_genome_filename,
self.min_depth, self.min_bqual, self.min_mqual)
args_list.append(args_tuple)
counts_tuple_list = pool.map(process_by_segment, args_list)
paired_counts = []
BAF_counts = []
for counts_tuple_j in counts_tuple_list:
paired_counts_j, BAF_counts_j = counts_tuple_j
paired_counts.append(paired_counts_j)
BAF_counts.append(BAF_counts_j)
BAF_heatmap = BAFHeatMap(BAF_counts)
BAF_heatmap.write_heatmap(self.filename_base)
data = Data(self.segments, paired_counts)
data.tumor_LOH_test(self.WES_flag)
data.write_data(self.filename_base)
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)