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  1. def global_alignment_score(v, w, scoring_matrix, sigma):
  2.     '''Return the global alignment score of v and w subject to the given scoring matrix and indel penalty sigma.'''
  3.  
  4.     # Initialize the scoring matrix.
  5.     S = [[0 for j in xrange(len(w)+1)] for i in xrange(len(v)+1)]
  6.  
  7.     # Initialize the edges with the given penalties.
  8.     for i in xrange(1, len(v)+1):
  9.         S[i][0] = -i*sigma
  10.     for j in xrange(1, len(w)+1):
  11.         S[0][j] = -j*sigma
  12.  
  13.     # Fill in the Score and Backtrack matrices.
  14.     for i in xrange(1, len(v)+1):
  15.         for j in xrange(1, len(w)+1):
  16.             scores = [S[i-1][j] - sigma, S[i][j-1] - sigma, S[i-1][j-1] + scoring_matrix[v[i-1], w[j-1]]]
  17.             S[i][j] = max(scores)
  18.  
  19.     return S[len(v)][len(w)]
  20.  
  21. if __name__ == '__main__':
  22.     from scripts import BLOSUM62, ReadFASTA
  23.  
  24.     # Parse the two input protein strings.
  25.     s, t = [fasta[1] for fasta in ReadFASTA('rosalind_fibd.txt')]
  26.  
  27.     # Get the alignment score.
  28.     score = str(global_alignment_score(s, t, BLOSUM62(), 5))
  29.  
  30.     # Print and save the answer.
  31.     print score
  32.     with open('011_FIBD.txt', 'w') as output_data:
  33.       output_data.write(score)
  34.  
Runtime error #stdin #stdout #stderr 0s 23352KB
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Standard input is empty
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Standard output is empty
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Traceback (most recent call last):
  File "prog.py", line 22, in <module>
ImportError: No module named scripts
https://ideone.com/FIPuFl
language:
Python (cpython 2.7.16)
created:
7 years ago
visibility:
public

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