In [1]:

    

from skbio.alignment import local_pairwise_align_ssw
from skbio import DNA


    

In [2]:

    

W2_44 = DNA("AGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAGCGAGGCCCAACCACCCGCAAGGGTGGGGAAGGCCTAGCGGCGAACGGGTGAGTAACACGTGAGCAACCTGTCCCGAAGACCGGGATAACACCGGGAAACCGGTGCTAATACCGGATACCCCCTACGGATCGCATGGTCCGTCGAGGAAAGGATTCTGCTTCGGGAGGGGCTCGCGGCCTATCAGCTTGTTGGTGGGGTAACGGCCCACCAAGGCGTCGACGGGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGGGCGAAAGCCTGACGCAGCAACGCCGCGTGGGGGATGAAGGCCTTCGGGTTGTAAACCCCTTTCAGCAGGAACGAAATTGACGGTACCTGCAGAAGAAGCCCCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCGAGCGTTGTCCGGATTCATTGGGCGTAAAGAGCTCGTAGGCGGCTTGGCAAGTCGGGTGTGAAAACTTCAGGCTCAACCTGGGGATGCCACTCGATACTGCTATGGCTAGAGTCCGGTAGGGGACCACGGAATTCCTGGTGTAGCGGTGAAATGCGCAGAGATCAGGAGGAACACCGGTGGCGAAGGCGGTGGTCTGGGCCGGCACTGACGCTGAGGAGCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGGCCTTATCAACGGGTTCCGTGCCGCAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGCTTAATTCGAGGCAACGCGAAGAACCTTACCTGGGTTTGACATGTAGGGAAAAGCCGTAGAGATACGGTGTCCTTCGGGGCCTTACACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGACGACGTCAAGTCATCATGCCCCTTACGTCCAGGGCTGCACACATGCTACAATGGCCGGTACAAAGGGCTGCTATTCCGCGAGGATGAGCGAATCCCAAAAAGCCGGTCTCAGTTCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAGTCGCTAGTAATCCCGGATCAGCAACGCCGGGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTCGGCAACACCCGAAGCCGGTGGCCCAACCGCAAGGAGGGAGCCGTCGAAGGTGGGGTCGGTGATTGGGGTGAAG", "W2_44")

w3_15 = DNA("AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAGCGAGGTCCATCCGGTGGCAACACCGGGGAAGACCTAGCGGCGAACGGGTGAGTAACACGTGAGCAACCTGTCCCGAAGACCGGGATAACACCGGGAAACCGGTGCTAATACCGGATACCCTCTCCTGGCCGCATGGCCTAAAGAGGAAATGGATTCCGCTTCGGGAGGGGCTCGCGGGCTATCAGCTTGTTGGTGGGGTAACGGCCTACCAAGGCGACGACGGCTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGGGCGAAAGCCTGACGCAGCAACGCCGCGTGGGGGATGAGGGCCTTCGGGTTGTAAACCCCTTTCAGCAGGGACGAAATTGACGGTACCTGCAGAAGAAGCCCCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGCTTGGCAAGTCGGGTGTGAAACCTCCAGGCTCAACCTGGAGATGCCACTCGATACTGCTATGGCTAGAGTCCGGTAGGGGACCACGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGTGGTCTGGGCCGGCACTGACGCTGAGGAGCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAATGTTGGGCACTAGGTGTGGGGTCTTATCAACGGGCTCCGTGCCGTAGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGCTTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTGAACTACGCAGGAAAAGCCGTAGAGATACGGTGTCCGAAAGGGCCTGCGATAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTATGTTGCCAGCGGATCATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTGCACACATGCTACAATGGCCGGTACAAAGGGCTGCTATCCCGCGAGGGTGAGCGAATCCCATAAAGCCGGTCTCAGTTCGGATCGGAGTCTGCAACTCGACTCCGTGAAGTCGGAGTCGCTAGTAATCCCGAATCAGCAACGTCGGGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTTGGTAACACCCGAAGCCGGTGGCCCAACCGCAAGGAGGGAGCCGTCGAAGGTGGGATCAGCGATTGGGGTGAA", "w3_15")

q1 = DNA("TACGAGGGGGGCAAGCGTTGTTCGGAATTATTGGGCGTAAAGGGCGCGTAGGCGGTGCGGTAAGTCACCTGTGAAATCTCCGGGCTTAACTCGGAGCCTGCAGGCGAAACTGCCGTGCTTGAGTGTGGGAGAGGTGCGTGGAATTCCCGGT", "BAQ4166.3_54216")

q2 = DNA("TACGAGGGGGGCAAGCGTTGTTCGGAATTATTGGGCGTAAAGGGCGCGTAGGCGGTGCGGTAAGTCACCTGTGAAATCTCCGGGCTTAACTCGGAGCCTGCAGGCGAAACTGCCGTGCTTGAGTGTGGGAGAGGTGCGTGGAATTCCCGGT", "BAQ4166.3_54216")

q3 = DNA("TACGGGGGGGGCAAGCGTTGTTCGGAATTATTGGGCGTAAAGGGCGCGTAGGCGGTGCGGTAAGTCTTCTGTGAAAACTCCGGGCTCAATTCGGAGCCTGCAGGGGAAACTGCCGTGCTGGAGTGTGGGAGAGGTGAGTGGAATTCCCGGG", "BAQ2420.1.2_3247082")


    

In [3]:

    

for q in [q1, q2, q3]:
    for s in [W2_44, w3_15]:
        a = local_pairwise_align_ssw(q, s)
        print(q.id, s.id, a[0].fraction_same(a[1]), a.sequence_length())


    

    




('BAQ4166.3_54216', 'W2_44', 0.71895424836601307, 153)
('BAQ4166.3_54216', 'w3_15', 0.75163398692810457, 153)
('BAQ4166.3_54216', 'W2_44', 0.71895424836601307, 153)
('BAQ4166.3_54216', 'w3_15', 0.75163398692810457, 153)
('BAQ2420.1.2_3247082', 'W2_44', 0.8089887640449438, 89)
('BAQ2420.1.2_3247082', 'w3_15', 0.84269662921348321, 89)

In [ ]: