How to get % similarity between strains and mutation files
left_lineagelist = [x.split('_')[-1].split('|')[0] 
                          for x in left_lineagelist]
        right_lineagelist = set([x.split('_')[-1].split('|')[0] 
                          for x in right_lineagelist])

Allows for extraction of 6 digit EPI, provided the file has had sequences removed prior; as such:
for line in lines:
    if line[0] == '&gt;':
        print(line[1:])