I am wondering how I can get sequence indices from a BioAlignments.jl alignment. The pairalign function returns an object from which I can get the sequences of the aligned region and the score. And while the function prints out the starting indices of the aligned region, I don’t know how to access those values.
using BioAlignments
using BioSequences
scoremodel = AffineGapScoreModel(EDNAFULL, gap_open=-5, gap_extend=-1);
my_alignment = pairalign(LocalAlignment(),dna"ATATTAGGTATTGATTATTGTACGCGGCCCGGC" , dna"TTGATTATTGT", scoremodel)
alignment(my_alignment)