def last_part():
the_donors = msgpack.load(file('donors_{}'.format(c.DATASET),'rb'))
#clean up
the_donors = [donors for donors in the_donors if donors]
good_changes = []
for donor_tuple in the_donors:
donor = donor_tuple[1]
pos = donor_tuple[0]
ref_piece = ref[pos:pos+len(donor)]
changes, score = dependencies.identify_changes(ref_piece,donor,0)
if score < 10:
#print visualize_lines(donor,pos,ref_piece)
for cc in changes:
try:
cc[3] += pos
except:
cc[2] += pos
good_changes.extend(changes)
utils.write_indels(good_changes, DO_NUMBER)
#clean up
the_donors = [donors for donors in the_donors if donors]
# all_snp(d, ref)
#msgpack.dump(the_donors,file('donors_{}'.format(c.DATASET),'wb'))
#exit()
#
good_changes = []
for donor_tuple in the_donors:
donor = donor_tuple[1]
pos = donor_tuple[0]
ref_piece = ref[pos:pos+len(donor)]
changes, score = dependencies.identify_changes(ref_piece,donor,-1)
if score < len(donor) * 0.4: # thanks leah
#visualize_lines(donor,pos,ref, pos)
#print 'C.\n{}'.format(changes)
for cc in changes:
try:
if cc[2] == '.':
changes.remove(cc)
continue
cc[3] += pos
except:
cc[2] += pos
good_changes.extend(changes)
for _ in good_changes:
