def gaff(f, score=ra.BLOSUM62, gap_init= -11, gap_ext= -1, debug=False): '''Main driver to solve the GAFF problem.''' x, y = ro.fafsa_values(f) d, (xx, yy) = ra.optimal_alignment(x, y, score, gap_init, gap_ext, debug=debug) print d print xx print yy
def sims(f, debug=False, align="fit"): """Main driver to solve the SIMS problem.""" (s, t), score, gap_score = ro.fafsa_values(f), ra.FixedCost(1, -1), -1 d, (ss, tt) = ra.optimal_alignment(s, t, score, gap_score, gap_score, align=align, debug=debug) print d print ss print tt
def gcon(f, debug=False): '''Main driver to solve the GCON problem.''' x, y = ro.fafsa_values(f) d, (xx, yy) = ra.optimal_alignment(x, y, ra.BLOSUM62, -5, 0, debug=debug) print d print xx print yy return d
def loca(f, debug=False): '''Main driver to solve the LOCA problem.''' x, y = ro.fafsa_values(f) d, (xx, yy) = ra.optimal_alignment(x, y, ra.PAM250, -5, -5, align='local', debug=debug, gap_symbol='') return ro.join_list((d, xx, yy), delimiter='\n')