gistfile1.py

protein = "beta2"
fingerprint = "KlekFP"

# Read data, not important
actives, inactives = get_protein_fingerprint_cluster_files(protein, fingerprint)
clusters_active = []
for a, _ in actives:
    clusters_active.append(pd.io.parsers.read_csv(os.path.join(c["DATA_DIR"], a), header=None).as_matrix().astype("float32"))
inactive = pd.io.parsers.read_csv(os.path.join(c["DATA_DIR"], inactives), header=None).as_matrix().astype("float32")

print "Sizes: ", [cl.shape[0] for cl in clusters_active]

# Report when found shared example
for A, B in product(clusters_active, clusters_active):
    if A is not B:
        # Distances between cluster A and B using L1
        D = np.min(pairwise_distances(A, B, metric='l1'), axis=1)
        print "Shared examples: ", (D==0).sum()
        print "A.shape[0]=", A.shape[0], "B.shape[0]=", B.shape[0]
"""
OUT:

Sizes:  [408, 548, 548, 22, 2, 114]
Shared examples :  408
A.shape[0]= 408 B.shape[0]= 548
Shared examples :  408
A.shape[0]= 408 B.shape[0]= 548
Shared examples :  0
A.shape[0]= 408 B.shape[0]= 22
Shared examples :  0
A.shape[0]= 408 B.shape[0]= 2
Shared examples :  0
A.shape[0]= 408 B.shape[0]= 114
Shared examples :  408
A.shape[0]= 548 B.shape[0]= 408
Shared examples :  546
A.shape[0]= 548 B.shape[0]= 548
Shared examples :  22
A.shape[0]= 548 B.shape[0]= 22
Shared examples :  2
A.shape[0]= 548 B.shape[0]= 2
Shared examples :  114
A.shape[0]= 548 B.shape[0]= 114
Shared examples :  408
A.shape[0]= 548 B.shape[0]= 408
Shared examples :  546
A.shape[0]= 548 B.shape[0]= 548
Shared examples :  22
A.shape[0]= 548 B.shape[0]= 22
Shared examples :  2
A.shape[0]= 548 B.shape[0]= 2
Shared examples :  114
A.shape[0]= 548 B.shape[0]= 114
Shared examples :  0
A.shape[0]= 22 B.shape[0]= 408
Shared examples :  22
A.shape[0]= 22 B.shape[0]= 548
Shared examples :  22
A.shape[0]= 22 B.shape[0]= 548
Shared examples :  0
A.shape[0]= 22 B.shape[0]= 2
Shared examples :  0
A.shape[0]= 22 B.shape[0]= 114
Shared examples :  0
A.shape[0]= 2 B.shape[0]= 408
Shared examples :  2
A.shape[0]= 2 B.shape[0]= 548
Shared examples :  2
A.shape[0]= 2 B.shape[0]= 548
Shared examples :  0
A.shape[0]= 2 B.shape[0]= 22
Shared examples :  0
A.shape[0]= 2 B.shape[0]= 114
Shared examples :  0
A.shape[0]= 114 B.shape[0]= 408
Shared examples :  114
A.shape[0]= 114 B.shape[0]= 548
Shared examples :  114
A.shape[0]= 114 B.shape[0]= 548
Shared examples :  0
A.shape[0]= 114 B.shape[0]= 22
Shared examples :  0
A.shape[0]= 114 B.shape[0]= 2
"""