def compare_with_source(source_fname, realigned_fname, seq1, seq2):
d = DataLoader()
src = d.getSequences(source_fname, [seq1+'$', seq2+'$'])
realigned = d.getSequences(realigned_fname, [seq1+'$', seq2+'$'])
src_f = create_alignemnt_function(src)
realigned_f = create_alignemnt_function(realigned)
l = max(len(src[0]), len(realigned[0]))
s = 0
for i in range(min(len(src[0]), len(realigned[0]))):
if src_f(i) == realigned_f(i):
s += 1
return float(s)/l
def score(fname):
sequence_names = ['sequence1', 'sequence2', 'sequence3']
sequences = []
# fname = 'data/sequences/simulated_alignment.{}_{}.realigned.fa'
d = DataLoader()
for x in range(len(sequence_names)-1):
for y in range(x+1, len(sequence_names)):
sX = sequence_names[x]
sY = sequence_names[y]
if sX != sY:
sequences.append(d.getSequences(
fname.format(sX, sY), [sX+'$', sY+'$'])
)
return compare(*sequences)
