TE_consensus.py

def base_consensus(alignment, base_index):
    """ """
    # get the bases at this position, store in case we want to come back 
    # and assign the first one as th winner
    #n_seqs = len(alignment)
    bases = [r[base_index].upper() for r in alignment]
    base_c = Counter(bases)
    max_count = max(base_c.values())
    most_common_base  = [b for b in base_c.items() if b[1] == max_count]
    if len(most_common_base) == 1:
        return(most_common_base[0][0])
    tied_bases = [base for base,count in most_common_base]
    #this is where the logic of choosing the best base goes
    return(tied_bases[0])

def make_consensus(alignment):
    new_string = ""
    for base_index in range(alignment.get_alignment_length()):
        new_string += base_consensus(alignment, base_index)
    return("".join(new_string))


#alignment = AlignIO.read("coi_ali.fna", "fasta")
#make_consensus(alignment)