sbwt 0.4.2

Indexing sets of DNA k-mers with the spectral Burrow-Wheeler transform.
Documentation 
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import sys

seqs = ["TGTTTG", "TTGCTAT", "ACGTAGTATAT", "TGTAAA"]
k = 4

kmers = []
source_kmer_set = set()

for T in seqs:
    for i in range(len(T)-k+1):
        kmers.append(T[i:i+k])

for T in seqs:
    for i in range(len(T)-k+1):
        x = T[i:i+k]
        if all([(c + x[0 : k-1]) not in kmers for c in "ACGT"]):
            source_kmer_set.add(x)
            for j in range(k-1):
                x = '$' + x[0 : k-1]
                kmers.append(x)
kmers.append("$"*k)
kmers = list(set(kmers)) # Remove duplicates
kmers.sort(key = lambda x : x[::-1]) # colex

kmer_set = set(kmers)

print("digraph {")
print("rankdir=LR;") # Left to right layout
print("node [shape=rect];")
for i, x in enumerate(kmers):
    if x in source_kmer_set:
        print('{} [label="{}", fillcolor="lightblue", style="filled"];'.format(i, x))
    elif '$' in x:
        print('{} [label="{}", fillcolor="goldenrod1", style="filled"];'.format(i, x))
    else:
        print('{} [label="{}"];'.format(i, x))
for i, x in enumerate(kmers):
    edges = []
    x_other_set = [d + x[1:] for d in "$ACGT" if (d + x[1:]) in kmer_set]
    for c in "ACGT":
        y = (x[1:] + c)
#        print(x,y,x_other_set)
        if y in kmer_set:
            j = kmers.index(y)
            if x == min(x_other_set): 
                print('{} -> {} [label = "{}"];'.format(i, j, y[-1]))
            else:
                print('{} -> {} [style = "dashed", color="red", fontcolor="red", label = "{}"];'.format(i, j, y[-1]))
            
print("}")