INNER CODE UNIT · Python

affine_pen

cbg-ethz/V-pipe · workflow/scripts/alignmentBias.py:149

    affine_pen = pairwise2.affine_penalty(-1, -0.1, True)
    with open(args.haplotype_seqs, "r") as infile:
        for record in SeqIO.parse(infile, "fasta"):
            alignment = pairwise2.align.globalmc(
                reference.seq,
                record.seq,
                1,
                0,
                affine_pen,
                affine_pen,
                one_alignment_only=True,
            )
            divergence[record.id] = (
                hamming_dist(alignment[0][0], alignment[0][1]) / alignment[0][4]
            )

    with open(args.output_file, "w") as outfile:
        outfile.write(

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