def test(self):
alignment = [
"AAAagaattcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT"
"AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT"
"TTAGTGAAAATGGAGGATCAAGTagAtTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT"
"GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC"
"AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC",
"AAAagaTttcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT"
"AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT"
"TTAGTGAAAATGGAGGATCAAGTagctTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT"
"GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC"
"AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC",
"AAAagaTttcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT"
"AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT"
"TTAGTGAAAATGGAGGATCAAGTagctTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT"
"GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC"
"AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC",
]
self.assertEqual(len(alignment), 3)
enzymes = [EcoRI, AluI]
align = createAlignment(alignment, Alphabet.generic_dna)
map = CAPS.CAPSMap(align, enzymes)
self.assertEqual(len(map.dcuts), 2)
self.assertEqual(map.dcuts[0].enzyme, EcoRI)
self.assertEqual(map.dcuts[0].start, 5)
self.assertEqual(map.dcuts[0].cuts_in, [0])
self.assertEqual(map.dcuts[0].blocked_in, [1, 2])
self.assertEqual(map.dcuts[1].enzyme, AluI)
self.assertEqual(map.dcuts[1].start, 144)
self.assertEqual(map.dcuts[1].cuts_in, [1, 2])
self.assertEqual(map.dcuts[1].blocked_in, [0])
def testNoCAPS(self):
alignment = ["aaaaaaaaaaaaaaaaaaaa",
"aaaaaaaaaaaaaaaaaaaa",
]
enzymes = []
align = createAlignment(alignment, Alphabet.generic_nucleotide)
map = CAPS.CAPSMap(align, enzymes)
self.assertEqual(map.dcuts, [])
def test_trivial(self):
enzymes = [EcoRI]
alignment = ["gaattc", "gaactc"]
align = createAlignment(alignment, Alphabet.generic_dna)
map = CAPS.CAPSMap(align, enzymes)
self.assertEqual(len(map.dcuts), 1)
self.assertEqual(map.dcuts[0].enzyme, EcoRI)
self.assertEqual(map.dcuts[0].start, 1)
self.assertEqual(map.dcuts[0].cuts_in, [0])
self.assertEqual(map.dcuts[0].blocked_in, [1])
def testNoCAPS(self):
alignment = ["aaaaaaaaaaaaaaaaaaaa", "aaaaaaaaaaaaaaaaaaaa"]
enzymes = []
align = createAlignment(alignment)
map = CAPS.CAPSMap(align, enzymes)
self.assertEqual(map.dcuts, [])