import numpy as np

#Defining needleman wunsch  algorithimn

def needleman_wunsch(seq1, seq2, match_score=1, mismatch_score=-1, gap_penalty=-1):
    m, n = len(seq1), len(seq2)

    # Create the score matrix and initialize the first row and column
    score_matrix = np.zeros((m + 1, n + 1), dtype=int)

    for i in range(m + 1):
        score_matrix[i, 0] = i * gap_penalty

    for j in range(n + 1):
        score_matrix[0, j] = j * gap_penalty

    # Fill in the score matrix
    for i in range(1, m + 1):
        for j in range(1, n + 1):
            match = score_matrix[i - 1, j - 1] + (match_score if seq1[i - 1] == seq2[j - 1] else mismatch_score)
            delete = score_matrix[i - 1, j] + gap_penalty
            insert = score_matrix[i, j - 1] + gap_penalty
            score_matrix[i, j] = max(match, delete, insert)

    # Traceback to find the alignment
    align1, align2 = '', ''
    i, j = m, n

    while i > 0 or j > 0:
        current_score = score_matrix[i, j]
        if i > 0 and score_matrix[i - 1, j] + gap_penalty == current_score:
            align1 = seq1[i - 1] + align1
            align2 = '-' + align2
            i -= 1
        elif j > 0 and score_matrix[i, j - 1] + gap_penalty == current_score:
            align1 = '-' + align1
            align2 = seq2[j - 1] + align2
            j -= 1
        else:
            align1 = seq1[i - 1] + align1
            align2 = seq2[j - 1] + align2
            i -= 1
            j -= 1

    return score_matrix[m, n], align1, align2

# Example usage:
seq1 = "AAAATTAC"
seq2 = "TATGC"
score, aligned_seq1, aligned_seq2 = needleman_wunsch(seq1, seq2)

print(f"Alignment Score: {score}")
print(f"Aligned Sequence 1: {aligned_seq1}")
print(f"Aligned Sequence 2: {aligned_seq2}")



# Tried but was not able to create a blosum matrix it giving the error still uploading the file that code didnot work.