def scheme2(kmer):
'''
BWT, 3 bit alphabet
Encoding scheme =
encoding := bases
bases := 3 bits for base, 1 bit for RLE, 4 bits for len 2-17
Examples: AC == 0000 0010
AAC == 00010000 0010
AAAC == 00010001 0010
AAAAC == 00010010 0010
AAAAAC == 00010011 0010
Two-tiered encoding, run len 1 => 4 bits, run len 2-17 => 8 bits
'''
trans_kmer = bwt.bwt(kmer)
size = 0
i = 0
while i < len(trans_kmer):
run_length = run_len(trans_kmer, i)
if run_length == 1:
size += 4
else:
size += 8
if run_length > 17:
run_length = 17
i += run_length
return size
def scheme1(kmer):
'''
BWT, EOL, 2 bit alphabet
Encoding scheme =
encoding := eol_pos bases
eol_pos := 6 bits for eol, suitable for k <=~ 63
bases := 2 bits for base, 1 bit for RLE, 1 bit for len 2-3, (1 bit for len 2-3 | 6 bits for len <= 63)
Examples: AC == 000 010
AAC == 00100 010
AAAC == 00101 010
AAAAC == 0011000000 010
AAAAAC == 0011000001 010
Three-tiered encoding, run len 1 => 3 bits, run len 2-3 => 5 bits, run len 4-68 => 10 bits
'''
trans_kmer, eol_idx = bwt.eol_format(bwt.bwt(kmer))
size = 0
size += 6
i = 0
while i < len(trans_kmer):
run_length = run_len(trans_kmer, i)
if run_length == 1:
size += 3
elif run_length in [2,3]:
size += 5
else:
size += 10
if run_length > 68:
run_length = 68
i += run_length
return size
def main():
chunks = []
with open(FILENAME, 'rb') as f:
for _ in range(MAX_NUM_CHUNKS):
c = f.read(MAX_CHUNK_SIZE)
if not c:
break
chunks.append(c)
print('Original:')
matrix = compute_distance_matrix(chunks, verbose=True)
# print(matrix)
print('After BWT:')
chunks_bwt = [bwt(c) for c in chunks]
matrix_bwt = compute_distance_matrix(chunks_bwt, verbose=True)
def scheme3(kmer):
'''
2 bit alphabet, BWT, MTF, shitty huffman encoding, 0 => 1, 1 => 01, 2 => 000, 3 => 001
Add 6 bits for eol position
'''
def huff_size(c):
return { 0: 1,
1: 2,
2: 3,
3: 3,
}[c]
trans_kmer, eol_idx = bwt.eol_format(bwt.bwt(kmer))
trans_kmer = mtf.mtf(trans_kmer)
size = 0
size += 6
i = 0
while i < len(trans_kmer):
size += huff_size(trans_kmer[i])
i += 1
return size
def scheme5(kmer):
'''
3 bit alphabet, BWT, MTF, shitty huffman encoding, 0 => 1, 1 => 01, 2 => 000, 3 => 0011, 4 => 0010
Add 6 bits for eol position
modified MTF to not push to front when base is N
'''
def huff_size(c):
return { 0: 1,
1: 2,
2: 3,
3: 4,
4: 4,
}[c]
trans_kmer, eol_idx = bwt.eol_format(bwt.bwt(kmer))
trans_kmer = mtf.mtf_n(trans_kmer)
size = 0
size += 6
i = 0
while i < len(trans_kmer):
size += huff_size(trans_kmer[i])
i += 1
return size
def main(args):
#args = sys.argv[1:]
if len(args) != 3:
print "Please enter the right number of arguments"
exit()
inputFile = open(args[1],'r')
inputFileReadLine = inputFile.readline()
inputFileReadLine = inputFileReadLine[1:len(inputFileReadLine)-1]
S = inoutPut.inputToList(inputFile)
lengthS = len(S)
inputFile.close()
if args[0] == '-bwt':
print "bwt of:", inputFileReadLine
newT = util.convertToNumAlphabet(S)
s_array = ks.cd3(newT)
S += ["$"]
b_wt = bwt.bwt(S,s_array)
outputFile = open(args[2],'w')
inoutPut.outputToFile(outputFile, b_wt, 'bwt', inputFileReadLine)
outputFile.close()
print "length of string:", lengthS
print "For BWT Check file:", args[2]
elif args[0] == '-ibwt':
print "ibwt of:", inputFileReadLine
rec = bwt.ibwt(S)
outputFile = open(args[2],'w')
inoutPut.outputToFile(outputFile, rec,'ibwt', inputFileReadLine)
outputFile.close()
print "length of string:", lengthS
print "For iBWT Check file:", args[2]
else:
print "You must indicate whether we are doing -btw or -ibtw"
exit()
pass
from bwt import bwt
from bwtinverse import inverse_bwt
from text_generator import text_gen
ERROR_THRESHOLD = 0.1
if __name__ == '__main__':
stop = 1000
total = 0
err = 0
while True:
total += 1
text = text_gen()
bwt_text = bwt(text)
text1 = inverse_bwt(bwt_text)
if text != text1:
err += 1
print('test1 get bwt')
print('text = {}, text1 = {}'.format(text, text1))
print('bwt = {}'.format(bwt_text))
if total * ERROR_THRESHOLD <= err and err > 0 or total >= stop:
break
if total % 100 == 0:
print('total = {}, err = {}'.format(total, err))