class BamToDataConverter:
def __init__(self, normal_bam_filename, tumor_bam_filename,
reference_genome_filename, input_filename_base, segments_bed,
min_depth=20, min_bqual=10, min_mqual=10, process_num=1):
self.normal_bam_filename = normal_bam_filename
self.tumor_bam_filename = tumor_bam_filename
self.reference_genome_filename = reference_genome_filename
self.input_filename_base = input_filename_base
self.segments_bed = segments_bed
self.min_depth = min_depth
self.min_bqual = min_bqual
self.min_mqual = min_mqual
self.process_num = process_num
self.data = Data()
def convert(self):
self._load_segments()
self._get_counts()
self._get_LOH_frac()
data_file_name = self.input_filename_base + '.MixClone.input.pkl'
outfile = open(data_file_name, 'wb')
pkl.dump(self.data, outfile, protocol=2)
outfile.close()
def _load_segments(self):
normal_bam = pysam.Samfile(self.normal_bam_filename, 'rb')
tumor_bam = pysam.Samfile(self.tumor_bam_filename, 'rb')
print 'Loading segments by {0}...'.format(self.segments_bed)
sys.stdout.flush()
self.data.load_segments(normal_bam, tumor_bam, self.segments_bed)
normal_bam.close()
tumor_bam.close()
def _get_counts(self):
seg_num = self.data.seg_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.data.segments[j].name
chrom_name = self.data.segments[j].chrom_name
chrom_idx = self.data.segments[j].chrom_idx
start = self.data.segments[j].start
end = self.data.segments[j].end
args_tuple = (seg_name, chrom_name, chrom_idx, 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)
for j in range(0, seg_num):
paired_counts_j, BAF_counts_j = counts_tuple_list[j]
self.data.segments[j].paired_counts = paired_counts_j
self.data.segments[j].BAF_counts = BAF_counts_j
def _get_LOH_frac(self):
self.data.get_LOH_frac()
