CODEWITHSUNDEEP
pythonalignment
user3216969
user3216969

Reputation: 169

Evaluate a multiple sequence alignment

I am using python to doing multiple sequence alignment.for evaluate the alignment I use Weighted sum of pairs score (WSP) for three sequences seq1, seq2 and seq3, as we know the score is calculate as follows: first calculate the score of (seq1,seq2), and score of(seq1,seq3) and score of (seq2,seq3)

WSP=score(seq1,seq2)+score(seq1,seq3)+score(seq2,seq3)

python code:

def wsp():
        w=1
        dis=sum_distance(seq1,seq2,seq3)
        wsp=w*dis
        return wsp

now, I want to use a fasta file which contains many sequences.how can I calculate the WSP score for all sequences in a fasta file.

where sum_distance is a function to calculate distances between sequences

Upvotes: 2

Views: 1095

Answers (1)

scezar
scezar

Reputation: 46

The simplest way is to run sum_distance function over each pair of sequences in your file: 

total_distance = 0  
with open('yourfile.fa', 'r') as sequences_list_1:
    for key_1, seq_1 in enumerate(sequences_list_1):
        with open('yourfile.fa', 'r') as sequences_list_2:
            for key_2, seq_2 in enumerate(sequences_list_2):
                if key_1 < key_2:
                    total_distance += sum_distance(seq_1, seq_2)

Upvotes: 1

Related Questions