# shortest path alignement python

I have this function to find the shortest path in a matrix from M[0][0] to M[m][n] i created the matrix and everything i want to draw the shortest path everything in working yet aseq1, and aseq2 are empty im unable to locate the problem

``````def path(seq1,seq2,matrix,gap):
aseq1 = ''
aseq2 = ''

#reconstruction de l'alignement aseq1 pour la premiere sequence et aseq2 pour la deuxieme
i = len(seq1[0])-1
j = len(seq2[1])-1
while i>0 and j>0:

if i%10==0:
stderr.write('.')

#utilisation de la matrice remplie pour tracer le chemin le plus court de M[0][0] a M[m][n]
score = M[i][j]
score_diag = M[i-1][j-1]
score_up = M[i][j-1]
score_left = M[i-1][j]

if score == score_diag + d[[seq1[i-1]][seq2[j-1]]]:
aseq1 = seq1[i-1] + aseq1
aseq2 = seq2[j-1] + aseq2
i -= 1
j -= 1
if score == score_left + gap:
aseq1 = seq1[i-1] + aseq1
aseq2 = '-' + aseq2
i -= 1
elif score == score_up + gap:
aseq1 = '-' + aseq1
aseq2 = seq2[j-1] + aseq2
j -= 1
else:
print("Erreur?")

while i>0:
# si j==0 avant i==0 on continue l'iteration avec i
aseq1 = seq1[i] + aseq1
aseq2 = '-' + aseq2
i -= 1

while j>0:
# si i==0 avant j==o on continue l'iteration avec j
aseq1 = '-' + aseq1
aseq2 = seq2[j] + aseq2
print (aseq1,aseq2)
j -= 1
print(aseq1,aseq2)
return (aseq1,aseq2)
``````

On Best Solutions

Pay attention to indentation in Python. All of the code inside the first `while` loop is inside `if i%10==0`. If `i` is ever not divisible by 10, the program will loop forever.

This is what I'm talking about. Compare the tabbing to your code above:

``````while i>0 and j>0:
if i%10==0:
stderr.write('.')

#by performing a traceback of how the matrix was filled out above,
#i.e. we find a shortest path from a[n,m] to a[0,0]
score = M[i][j]
score_diag = M[i-1][j-1]
score_up = M[i][j-1]
score_left = M[i-1][j]
``````