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Edit Distance
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Edit Distance
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import sys
from Bio import SeqIO
fopen=open(sys.argv[1])
data=[]
for seq_records in SeqIO.parse(fopen,"fasta"):
data.append(str(seq_records.seq))
s1=data[0]
s2=data[1]
def levenshteindistance(s,t):
#for all i and j, d[i,j] will hold the Levenshtein distance between
#the first i characters of s and the first j characters of t
m=len(s)+1
n=len(t)+1
#declare int d[0..m+1, 0..n+1]
d=[[0 for x in range(n)] for x in range(m)]
#set each element in d to zero
#source prefixes can be transformed into empty string by
#dropping all characters
for i in range(1, m):
d[i][0] = i
#target prefixes can be reached from empty source prefix
#by inserting every character
for j in range(1, n):
d[0][j] = j
for j in range(1, n):
for i in range(1, m):
if s[i-1] == t[j-1]:
substitutionCost = 0
else:
substitutionCost = 1
d[i][j] = min(d[i-1][j] + 1, #deletion
d[i][j-1] + 1, #insertion
d[i-1][j-1] + substitutionCost) #substitution
## for r in range(m):
## print(d[r])
return d[i][j]
print(levenshteindistance(s1,s2))