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: