Another solution is to use the standard Unix tools:

grep -v '^>' test.fasta | tr -d '\n' | sed -e 's/\(.\)/\1\n/g' | sort | uniq -c | sort -rn

:-)

Here's one solution using standard Python library: itertools. The code also works with multiple Fasta format.

from itertools import groupby

fh = open('file.fasta')

groups = (x[1] for x in groupby(fh, lambda l: l[0] == ">"))
for g in groups:
    header = next(g).strip()
    seq = ''.join(s.strip() for s in next(groups))
    counts = {}
    for s in [''.join(g) for k, g in groupby(seq)]:
        if s not in counts: counts[s] = 0
        counts[s]+=1
    print header
    print counts

It gives you:

>gi|7290019|gb|AAF45486.1| (AE003417) EG:BACR37P7.1 gene product [Drosophila melanogaster]
{'G': 1, 'RR': 1, 'LL': 1, 'M': 2, 'L': 1, 'II': 1, 'P': 1, 'R': 2, 'KKK': 1, 'X': 1}

One solution is to use an existing tool for this - like Biopieces www.biopieces.org) where you can do:

read_fasta -i test.faa | analyze_seq | analyze_vals -x

Try this. The getCount function will get you the single and consecutive amino acid counts

inFile = open('filePath','r')

def getCounts(seq):
    current = seq[0]
    counts = {}
    for i in range(1,len(seq), 1):
        if seq[i] != current[-1]:
            if not counts.has_key(current):
                counts[current] = 0
            counts[current] += 1
            current = seq[i]
        else:
            current += seq[i]
    return counts

header = ''
seq = ''
for line in inFile:
    if line[0] == ">":
        if header != '':
            print header + "\t" + str(getCounts(seq))
        header = line.strip()[1:]
        seq = ''
    else:
        seq += line.strip()
print header + "\t" + str(getCounts(seq))