matrix1 = [ [0,1,0,0,0,0,0,1,1,0],
[1,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0],
[0,0,1,1,1,1,1,0,0,1]
]
matrix2 = [ [10,0,10,3,5,5],
[0,5,0,3,5,0,5],
[0,1,0,3,0,5,0],
[0,4,0,1,0,0,5]
]
results = MOODS.search(seq, [matrix1, matrix2], 0.011)
print("Matrix 1 results: "+ str(len(results[0])))
print("Matrix 2 results: "+ str(len(results[1])))
matrices = [matrix1, matrix2]
thresholds = [0.011, 0.011]
bg = MOODS.bg_from_sequence(seq, 0.1)
q = 7
absolute_threshold = False
both_strands=False
ms = MOODS.MOODSSearch(matrices, thresholds, bg, q, absolute_threshold, both_strands)
results = ms.search(seq)
print("New Matrix 1 results: "+ str(len(results[0])))
print("New Matrix 2 results: "+ str(len(results[1])))
ms2 = MOODS.MOODSSearch(matrices, thresholds, bg, q, absolute_threshold, both_strands)
print(DIST_DIR)
fasta_filepath = join(DIST_DIR, "examples/data/sequence/dnaACGT.txt")
records = fasta.parseFasta(fasta_filepath)
seq = records[0][1]
matrix1 = [[0, 1, 0, 0, 0, 0, 0, 1, 1, 0], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 1, 1, 1, 1, 0, 0, 1]]
matrix2 = [[10, 0, 10, 3, 5, 5], [0, 5, 0, 3, 5, 0, 5], [0, 1, 0, 3, 0, 5, 0],
[0, 4, 0, 1, 0, 0, 5]]
results = MOODS.search(seq, [matrix1, matrix2], 0.011)
print("Matrix 1 results: " + str(len(results[0])))
print("Matrix 2 results: " + str(len(results[1])))
matrices = [matrix1, matrix2]
thresholds = [0.011, 0.011]
bg = MOODS.bg_from_sequence(seq, 0.1)
q = 7
absolute_threshold = False
both_strands = False
ms = MOODS.MOODSSearch(matrices, thresholds, bg, q, absolute_threshold,
both_strands)
results = ms.search(seq)
print("New Matrix 1 results: " + str(len(results[0])))
print("New Matrix 2 results: " + str(len(results[1])))
ms2 = MOODS.MOODSSearch(matrices, thresholds, bg, q, absolute_threshold,
both_strands)
