def get_bases( ref_base, call_string, qual_string, min_qual ):
bases = parse_call_string( ref_base, call_string )
quals = np.fromstring( qual_string, dtype=np.byte ) - ascii_offset
bases = np.array( bases )
bases = bases[quals >= min_qual]
return bases
def main( args ):
if args.bzip2:
mpileup_file = bz2.BZ2File( args.mpileup_file_name )
else:
mpileup_file = open( args.mpileup_file_name )
reader = get_reader( mpileup_file )
mcnt_file = MultinomialCountsFile( args.mcnt_file_name, 'w' )
rows = {}
i = 0
for row in reader:
chr_name = row['chr_name']
if chr_name not in rows:
rows[chr_name] = []
chr_coord = int( row['chr_coord'] )
normal_depth = int( row['normal_depth'] )
tumour_depth = int( row['tumour_depth'] )
ref_base = row['ref_base'].upper()
# Skip lines below coverage threshold.
if normal_depth < args.min_depth or tumour_depth < args.min_depth:
continue
normal_bases = parse_call_string( ref_base, row['normal_call_string'] )
tumour_bases = parse_call_string( ref_base, row['tumour_call_string'] )
normal_counter = Counter( normal_bases )
tumour_counter = Counter( tumour_bases )
normal_counts = []
tumour_counts = []
variant = True
for nucleotide in nucleotides:
nc = normal_counter[nucleotide]
tc = tumour_counter[nucleotide]
if nucleotide != ref_base:
if nc > 0 or tc > 0:
variant = True
normal_counts.append( nc )
tumour_counts.append( tc )
if sum( normal_counts ) < args.min_depth or sum( tumour_counts ) < args.min_depth:
continue
# Skip lines with no variants.
if not variant:
continue
mcnt_entry = [ chr_coord, ref_base ]
mcnt_entry.extend( normal_counts )
mcnt_entry.extend( tumour_counts )
rows[chr_name].append( mcnt_entry )
i += 1
if i >= 1e4:
print chr_name, chr_coord, mcnt_entry
write_rows( mcnt_file, rows )
rows = {}
i = 0
# Last call to write remaining rows.
write_rows( mcnt_file, rows )
mcnt_file.close()
