def parseClusterResult(result_file):
table = {}
transformer = BitWiseTransformer()
count = 0
header = ''
for line in open(result_file, 'r'):
count = count + 1
if count == 1:
print(line)
header = line.strip()
continue
parts = line.strip().split(',')
kmer = transformer.bitwise(int(parts[2]), 20)
if kmer in table:
print(','.join(table[kmer]))
print(line)
raise RuntimeError("duplicate found!\n")
else:
table[kmer] = parts
return (header,table)
def transform_2_seq(count_table_file, skip = 0):
table = {}
transformer = BitWiseTransformer()
count = 0
for line in open(count_table_file,'r'):
count = count + 1
if count <= skip:
continue
if ',' in line:
l = line.strip().split(',')
else:
l = line.strip().split('\t')
if len(l) == 3:
kmer = transformer.bitwise(int(l[0]),int(l[1]))
else:
kmer = transformer.bitwise(int(l[0]), 20)
if kmer in table:
print(','.join(table[kmer]))
print(line)
raise RuntimeError("duplicate found")
else:
table[kmer] = l
return table
#!/usr/bin/python
from bitwise import BitWiseTransformer
def extract_barcode(f,b_len):
table = {}
count = 0
for line in open(f, 'r'):
count = count + 1
if count == 1:
continue
parts = line.strip().split(',')
try:
if int(parts[1]) == b_len:
table[parts[0]] =parts[2]
except Exception as err:
print(parts[1])
print(parts)
return table
if __name__ == '__main__':
f = "../data/single_end_data/single_end_data_count.csv"
table = extract_barcode(f, 20)
output = open('../data/single_end_data/single_end_data_20_count.csv','w')
trans = BitWiseTransformer()
for k,v in table.items():
output.write(k + ',' + trans.bitwise(int(k),20) + ',' + v + '\n')
output.close()
def primers(f, l = 10): result = [] bt = BT() for i in range(f): result.append(bt.bitwise(i, l)) return result