I need to calculate the conservation or percentage of identity across several sequences in a multiple alignment (not pairwise but across all sequences). I wrote a function that works with clustal format where column conservation is marked with * (and therefore is just a matter of counting stars). I was wondering if someone would have an equivalent function for FASTA alignments.

def calc_ident(alignment_location):
    iden = 0.0 #Method1: Calculated divided by the total length of the multiple alignment
    iden2 = 0.0 #Method2: Calculated only with the positions suitable for evolutionary analysis (no gap in any sequence)
    f = open(alignment_location, "r")
    completo = f.read()
    stars = completo.count('*')
    f.close()
    handle = open(alignment_location, "rU")
    records = list(SeqIO.parse(handle, "clustal"))
    long_total = len(records[0].seq)
    iden = (stars*100/long_total)
    long_useful = calc_long(records) #Calculating length for score2
    if long_useful == 0: #Calculating score2
        iden2=0
    else:
        iden2 = (stars*100/long_useful)
    handle.close()
    return iden, iden2, long_total, long_useful

def calc_long(records):
    length = 0
    j=0
    while j<len(records[0].seq):
        i=0
        while i< len(records):
            if records[i].seq[j] == '-':
                break
            elif i==(len(records)-1):
                length += 1
            i+=1
        j+=1
    return length