for filename in sys argv sequences read_FASTA_sequences filename each

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for filename in sys.argv[1:]:
sequences = read_FASTA_sequences(filename)
#each sequence is a single cluster
#calc first table
A = np.zeros((len(sequences), len(sequences)))
for i in xrange(len(sequences):
for j in xrange(len(sequences)):
if i == j: continue
os.system("./pairwise " + sequences[i] + " " + sequences[j])