medvir/ecbc

Subtype assignment and primer (constant region) trimming for antibody sequences with Error Correcting BarCodes

ecbc's Issues

wobble consensus or max frequency in annotate_first.py

At the moment, annotate_first.py creates wobbles if the frequency is >= 25%
bases = ''.join(sorted([b for b, counts in c.items() if counts >= 0.25 * m]))

Partis does not accept wobbles (maybe accepts N). Therefore, a majority consensus should be generated, which I tried like this:
bases = ''.join(sorted(c, key=c.get, reverse=True)) bases = bases[0]

Does this make sense? Is there still need to include the 25% rule?

@merleschanz