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A generator for mapping of last to first column in BWT matrix. Input is a BW transform of DNA sequence.
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#change this if you want to support other types of sequences | |
def get_char_index(c): | |
if c == 'A': | |
return 1 | |
elif c == 'C': | |
return 2 | |
elif c == 'G': | |
return 3 | |
elif c == 'T': | |
return 4 | |
elif c == '$': | |
return 0 | |
else: | |
return -1 | |
def get_last_to_first(bwt): | |
counts = [0, 0, 0, 0, 0] | |
letter_pos = list() | |
for c in bwt: | |
index = get_char_index(c) | |
letter_pos.append(counts[index]) | |
counts[index] += 1 | |
cum_counts = [sum(counts[:i]) for i in range(len(counts))] | |
for i in range(len(bwt)): | |
letter_pos[i] += cum_counts[get_char_index(bwt[i])] | |
return letter_pos | |
def get_first_col(bwt): | |
letter_pos = get_last_to_first(bwt) | |
answer = [None] * len(bwt) | |
for i in range(len(bwt)): | |
answer[letter_pos[i]] = bwt[i] | |
return ''.join(answer) |
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More information about BW transform: Wikipedia.
A useful resource for this algorithm: Lecture from Stanford