def main( args ):
varscan_file_name = args.varscan_file_name
jcnt_file_name = args.jcnt_file_name
varscan_reader = csv.DictReader( open( varscan_file_name ), delimiter='\t' )
jcnt_file = JointCountsFile( jcnt_file_name, 'w' )
rows = {}
i = 0
for row in varscan_reader:
if row['var'] == '':
row['var'] = 'N'
chr_name = row['chrom']
if chr_name not in rows:
rows[chr_name] = []
chr_coord = int( row['position'] )
normal_ref_counts = int( row['normal_reads1'] )
tumour_ref_counts = int( row['tumor_reads1'] )
normal_non_ref_counts = int( row['normal_reads2'] )
tumour_non_ref_counts = int( row['tumor_reads2'] )
normal_counts = ( normal_ref_counts, normal_non_ref_counts )
tumour_counts = ( tumour_ref_counts, tumour_non_ref_counts )
ref_base = row['ref']
normal_non_ref_base = row['var']
tumour_non_ref_base = row['var']
jcnt_entry = [ chr_coord, ref_base, normal_non_ref_base, tumour_non_ref_base ]
jcnt_entry.extend( normal_counts )
jcnt_entry.extend( tumour_counts )
rows[chr_name].append( jcnt_entry )
print "\t".join( [str( x ) for x in jcnt_entry] )
i += 1
if i >= 1e4:
print chr_name, chr_coord
write_rows( jcnt_file, rows )
rows = {}
i = 0
# Last call to write remaining rows.
write_rows( jcnt_file, rows )
jcnt_file.close()
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 )
jcnt_file = JointCountsFile( args.jcnt_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 = get_bases(
ref_base,
row['normal_call_string'],
row['normal_base_qual_string'],
args.min_qual
)
tumour_bases = get_bases(
ref_base,
row['tumour_call_string'],
row['tumour_base_qual_string'],
args.min_qual
)
normal_non_ref_base, normal_counts = get_counts( ref_base, normal_bases )
tumour_non_ref_base, tumour_counts = get_counts( ref_base, tumour_bases )
# Check again for lines below read depth. The first check above speeds things up, though redundant.
d_N = normal_counts[0] + normal_counts[1]
d_T = tumour_counts[0] + tumour_counts[1]
if d_N < args.min_depth or d_T < args.min_depth:
continue
jcnt_entry = [ chr_coord, ref_base, normal_non_ref_base, tumour_non_ref_base ]
jcnt_entry.extend( normal_counts )
jcnt_entry.extend( tumour_counts )
rows[chr_name].append( jcnt_entry )
i += 1
if i >= 1e5:
print chr_name, chr_coord
write_rows( jcnt_file, rows )
rows = {}
i = 0
# Last call to write remaining rows.
write_rows( jcnt_file, rows )
jcnt_file.close()
mpileup_file.close()