def test_STree(self):
testSeqs = [
'10', 'mississippi', '10_10000', '4_3_10000', '4x3_10000',
'pc_10000'
]
for s in testSeqs:
print('.', end='', flush=True)
seq = tom.load(current_dir + s + '.seq.bz2')
f = bz2.BZ2File(current_dir + s + '.stree.bz2')
streeForm = pickle.load(f)
f.close()
symbolSize = 2 if seq.nInputSymbols() > 0 else 1
# create SuffixTree in several random steps:
sizes = sorted(
[rnd.randint(1,
seq.length() - 1)
for i in range(5)]) + [seq.length()]
stree = tom.STree(seq.sub(0, 0))
for sz in sizes:
stree.extendTo(seq.sub(0, sz))
self.assertTrue(
verifySuffixTreeCounts(seq.sub(0, sz), stree),
"!!! SuffixTree test NOT passed !!! Substring count discrepancy."
)
streeFormNew = canonicalizeSuffixTree(stree)
self.assertTrue(
verifySuffixTreeForm(seq, streeFormNew, streeForm),
"!!! SuffixTree test NOT passed !!! Something has changed.")
for l in range(1, min(seq.length(), 12)):
self.assertTrue(
tom.stree.Position(stree, seq.slice(-l)).isSuffix(),
".isSuffix() test failed!")
print(' ', end='', flush=True)
def test_wordsFromData(self):
testSeqs = ['10_10000', '4_3_10000', '4x3_10000', 'pc_10000']
for s in testSeqs:
print('.', end='', flush=True)
seq = tom.load(current_dir + s + '.seq.bz2')
stree = tom.STree(seq)
rstree = tom.STree(seq.reverse())
wordSettings = [(0,0,2**k,0) for k in range(4, 10)]
wordSettings += [(2,5,2**k,0) for k in range(4, 10)]
wordSettings += [(2,5,2**k,0) for k in range(4, 10)]
for wS in wordSettings:
XY = tom.wordsFromData(stree, *wS)
tom.sortWords(XY)
XYr = tom.wordsFromData(rstree, *wS)
tom.reverseWords(XYr)
tom.sortWords(XYr)
self.assertTrue(wordsAreEqual(XY, XYr),
"wordsFromData gives different results on reversed input for " + str(wS))
Y = tom.wordsFromData(stree, *wS, prefixUnique=True)
tom.sortWords(Y)
Yr = tom.wordsFromData(rstree, *wS, suffixUnique=True)
tom.reverseWords(Yr)
tom.sortWords(Yr)
self.assertTrue(wordsAreEqual(Y, Yr),
"wordsFromData gives different results on reversed input for characteristic words for " + str(wS))
Xr = tom.wordsFromData(rstree, *wS, prefixUnique=True)
tom.reverseWords(Xr)
tom.sortWords(Xr)
X = tom.wordsFromData(stree, *wS, suffixUnique=True)
tom.sortWords(X)
self.assertTrue(wordsAreEqual(X, Xr),
"wordsFromData gives different results on reversed input for indicative words for " + str(wS))
print(' ', end='', flush=True)
def test_wordsFromData(self):
testSeqs = ['10_10000', '4_3_10000', '4x3_10000', 'pc_10000']
for s in testSeqs:
print('.', end='', flush=True)
seq = tom.load(current_dir + s + '.seq.bz2')
stree = tom.STree(seq)
rstree = tom.STree(seq.reverse())
wordSettings = [(0, 0, 2**k, 0) for k in range(4, 10)]
wordSettings += [(2, 5, 2**k, 0) for k in range(4, 10)]
wordSettings += [(2, 5, 2**k, 0) for k in range(4, 10)]
for wS in wordSettings:
XY = tom.wordsFromData(stree, *wS)
tom.sortWords(XY)
XYr = tom.wordsFromData(rstree, *wS)
tom.reverseWords(XYr)
tom.sortWords(XYr)
self.assertTrue(
wordsAreEqual(XY, XYr),
"wordsFromData gives different results on reversed input for "
+ str(wS))
Y = tom.wordsFromData(stree, *wS, prefixUnique=True)
tom.sortWords(Y)
Yr = tom.wordsFromData(rstree, *wS, suffixUnique=True)
tom.reverseWords(Yr)
tom.sortWords(Yr)
self.assertTrue(
wordsAreEqual(Y, Yr),
"wordsFromData gives different results on reversed input for characteristic words for "
+ str(wS))
Xr = tom.wordsFromData(rstree, *wS, prefixUnique=True)
tom.reverseWords(Xr)
tom.sortWords(Xr)
X = tom.wordsFromData(stree, *wS, suffixUnique=True)
tom.sortWords(X)
self.assertTrue(
wordsAreEqual(X, Xr),
"wordsFromData gives different results on reversed input for indicative words for "
+ str(wS))
print(' ', end='', flush=True)
def test_STree(self):
testSeqs = ['10', 'mississippi', '10_10000', '4_3_10000', '4x3_10000', 'pc_10000']
for s in testSeqs:
print('.', end='', flush=True)
seq = tom.load(current_dir + s + '.seq.bz2')
f = bz2.BZ2File(current_dir + s + '.stree.bz2')
streeForm = pickle.load(f)
f.close()
symbolSize = 2 if seq.nInputSymbols() > 0 else 1
# create SuffixTree in several random steps:
sizes = sorted([rnd.randint(1, seq.length() - 1) for i in range(5)]) + [seq.length()]
stree = tom.STree(seq.sub(0,0))
for sz in sizes:
stree.extendTo(seq.sub(0,sz))
self.assertTrue(verifySuffixTreeCounts(seq.sub(0, sz), stree),
"!!! SuffixTree test NOT passed !!! Substring count discrepancy.")
streeFormNew = canonicalizeSuffixTree(stree)
self.assertTrue(verifySuffixTreeForm(seq, streeFormNew, streeForm), "!!! SuffixTree test NOT passed !!! Something has changed.")
for l in range(1, min(seq.length(), 12)):
self.assertTrue(tom.stree.Position(stree, seq.slice(-l)).isSuffix(), ".isSuffix() test failed!")
print(' ', end='', flush=True)