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import unittest
from Bio import CAPS
from Bio.Restriction import EcoRI, AluI
from Bio import Alphabet
from Bio.Align.Generic import Alignment
def createAlignment(sequences, alphabet):
"""Create an Alignment object from a list of sequences"""
align = Alignment(alphabet)
counter = 0
for sequence in sequences:
name = "sequence" + str(counter)
align.add_sequence(name, sequence)
counter+=1
return align
class TestCAPS(unittest.TestCase):
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 test(self):
alignment = [
"""\
AAAagaattcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT
AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT
TTAGTGAAAATGGAGGATCAAGTagAtTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT
GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC
AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC
""",
"""\
AAAagaTttcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT
AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT
TTAGTGAAAATGGAGGATCAAGTagctTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT
GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC
AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC
""",
"""\
AAAagaTttcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT
AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT
TTAGTGAAAATGGAGGATCAAGTagctTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT
GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC
AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC
""",
]
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_uneven(self):
alignment = ["aaaaaaaaaaaaaa",
"aaaaaaaa",
"aaaaaaaaaaaaaa",
]
align = createAlignment(alignment, Alphabet.generic_nucleotide)
self.assertRaises(CAPS.AlignmentHasDifferentLengthsError,
CAPS.CAPSMap,
align)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
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