def write_block(out, line, phase):
fields = line.strip().split()
metadata = parse_metadata(fields[3])
metadata['TR'] = 0.992 # empirical average
out.write('\t'.join(fields[0:3]))
out.write('\t' + metadata_to_str(metadata))
for f in fields[4:]:
fi = f.split(':')
pos = int(fi[0])
p0 = (int(fi[1]) + phase) % 2
p1 = (int(fi[2]) + phase) % 2
out.write('\t%d:%d:%d' % (pos, p0, p1))
out.write('\n')
fields = line.split()
chrom = fields[0]
pos = int(fields[1])
ph = int(fields[2])
true_phase[(chrom, pos)] = ph
num_switches = 0
num_long_switches = 0
num_transitions = 0
with open(args.blocks) as blocks:
for line in blocks:
pattern = ""
fields = line.split()
chrom = fields[0]
md = parse_metadata(fields[3])
for f in fields[4:]:
fi = f.split(':')
pos = int(fi[0])
p0 = int(fi[1])
if (chrom, pos) in true_phase:
pattern += str(int(p0 == true_phase[(chrom, pos)]))
# print md['ID'], '\t', pattern
if len(pattern) > 1:
corrected_pattern = correct_pattern(pattern)
num_block_switches = sum([1 for i in xrange(1,len(pattern)) if pattern[i] != pattern[i-1]])
num_long_block_switches = sum([1 for i in xrange(1,len(corrected_pattern))