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import os
import py2bit
import unittest
class Test(unittest.TestCase):
fname = os.path.dirname(py2bit.__file__) + "/py2bitTest/foo.2bit"
def testOpenClose(self):
tb = py2bit.open(self.fname, True)
assert(tb is not None)
tb.close()
def testChroms(self):
tb = py2bit.open(self.fname, True)
chroms = tb.chroms()
correct = {'chr1': 150, 'chr2': 100}
for k, v in chroms.items():
assert(correct[k] == v)
assert(tb.chroms("chr1") == 150)
assert(tb.chroms("c") is None)
tb.close()
def testInfo(self):
tb = py2bit.open(self.fname, True)
correct = {'file size': 161, 'nChroms': 2, 'sequence length': 250, 'hard-masked length': 150, 'soft-masked length': 8}
check = tb.info()
assert(len(correct) == len(check))
for k, v in check.items():
assert(correct[k] == v)
tb.close()
def testSequence(self):
tb = py2bit.open(self.fname, True)
assert(tb.sequence("chr1") == "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACGTACGTACGTagctagctGATCGATCGTAGCTAGCTAGCTAGCTGATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN")
assert(tb.sequence("chr1", 1, 2) == "N")
assert(tb.sequence("chr1", 1, 3) == "NN")
assert(tb.sequence("chr1", 0, 1000) == "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACGTACGTACGTagctagctGATCGATCGTAGCTAGCTAGCTAGCTGATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN")
assert(tb.sequence("chr1", 24, 74) == "NNNNNNNNNNNNNNNNNNNNNNNNNNACGTACGTACGTagctagctGATC")
tb.close()
def testBases(self):
tb = py2bit.open(self.fname, True)
assert(tb.bases("chr1") == {'A': 0.08, 'C': 0.08, 'T': 0.08666666666666667, 'G': 0.08666666666666667})
assert(tb.bases("chr1", 24, 74) == {'A': 0.12, 'C': 0.12, 'T': 0.12, 'G': 0.12})
assert(tb.bases("chr1", 24, 74, False) == {'A': 6, 'C': 6, 'T': 6, 'G': 6})
assert(tb.bases("chr2", 10, 20) == {'A': 0.2, 'C': 0.2, 'T': 0.3, 'G': 0.3})
assert(tb.bases("chr2", 10, 20, False) == {'A': 2, 'C': 2, 'T': 3, 'G': 3})
tb.close()
def testHardMaskedBlocks(self):
tb = py2bit.open(self.fname, True)
assert(tb.hardMaskedBlocks("chr1") == [(0, 50), (100, 150)])
assert(tb.hardMaskedBlocks("chr1", 25, 75) == [(0, 50)])
assert(tb.hardMaskedBlocks("chr1", 75, 100) == [])
assert(tb.hardMaskedBlocks("chr1", 75, 101) == [(100, 150)])
assert(tb.hardMaskedBlocks("chr2") == [(50, 100)])
tb.close()
def testSoftMaskedBlocks(self):
tb = py2bit.open(self.fname, storeMasked=True)
assert(tb.softMaskedBlocks("chr1") == [(62, 70)])
assert(tb.softMaskedBlocks("chr1", 0, 50) == [])
tb.close()
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