def test_cutoff():
g = GeneExpression(txs, ctrl_ids, case_ids)
x = np.array([[0, .1, .2, .3, .4, .5, .6, .7, .8, .9, 1],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1]])
assert np.all(g.cutoff(x, 45) == [[.45], [.5]])
assert np.all(g.cutoff(x, 80) == [[.8], [1]])
assert np.all(
g.cutoff(x, 16.34) == pytest.approx(np.array([[.1634], [0]]), .0001))
def parseExpression(ctrlFile, caseFile, genes, txs):
gene2tx = getGene2Tx(txs)
with open(ctrlFile, "r") as CTRL, open(caseFile, "r") as CASE:
idsCtrl = readSamples(CTRL)
idsCase = readSamples(CASE)
# gene -> xpr
expression = {}
for (tx, ctrl), (tx2, case) in zip(parseExpressionLine(CTRL),
parseExpressionLine(CASE)):
if tx != tx2:
raise SpadaError(
"Case and control expresion files mismatch: {} vs. {}.".
format(tx, tx2))
try:
gene = txs[tx]["gene_id"]
except KeyError:
continue
expression.setdefault(
gene, GeneExpression(gene2tx[gene], idsCtrl, idsCase))
expression[gene].addTx(tx, ctrl, case)
if expression[gene].isComplete:
yield gene, expression.pop(gene)
def test_init():
g = GeneExpression(txs, ctrl_ids, case_ids)
assert g._allTxs == txs
assert g._storedTxs == []
assert g._expressionCtrl.size == 0
assert g._expressionCase.size == 0
def test_isComplete():
expr = np.array([[2, 3, 4, 5]])
g = GeneExpression(txs, ctrl_ids, case_ids)
assert not g.isComplete
g.addTx('tx1', expr, expr)
assert not g.isComplete
g.addTx('tx2', expr, expr)
assert not g.isComplete
g.addTx('tx3', expr, expr)
assert g.isComplete
def test_computeExpectedDelta():
g = GeneExpression(txs, ctrl_ids, case_ids)
expr1 = np.array([[2, 3, 4, 5]])
expr2 = np.array([[6, 4, 2, 0]])
g.addTx('tx1', expr1, expr2)
g.addTx('tx2', expr1, expr2)
g.addTx('tx3', expr2, expr1)
psi_ctrl = np.array([[.5, .3, .4], [.3, .5, .15]])
wt_dpsi = g.computeExpectedDelta(psi=psi_ctrl)
assert wt_dpsi.shape == (2, 3)
assert np.all(wt_dpsi == pytest.approx(
np.array([[.2, .1, .1], [.2, .15, .35]]), .0001))
def test_addTx():
expr1 = np.array([[1.2, 3.4, 5.6]])
expr2 = np.array([[2.1, 4.3, 6.5]])
g = GeneExpression(txs, ctrl_ids, case_ids)
g.addTx('tx1', expr1, expr2)
assert np.all(g._expressionCtrl == expr1)
assert g._expressionCtrl.shape == (1, 3)
assert np.all(g._expressionCase == expr2)
assert g._expressionCase.shape == (1, 3)
assert g._storedTxs == ['tx1']
g.addTx('tx2', expr2, expr1)
assert np.all(g._expressionCtrl[1, :] == expr2)
assert g._expressionCtrl.shape == (2, 3)
assert np.all(g._expressionCase[1, :] == expr1)
assert g._expressionCase.shape == (2, 3)
assert g._storedTxs == ['tx1', 'tx2']
def test_matchExpressions():
expr1 = np.array([[2, 3, 4, 5]])
expr2 = np.array([[6, 4, 2, 0]])
g1 = GeneExpression(txs, ctrl_ids, ctrl_ids)
g1.addTx('tx1', expr1, expr2)
g1.addTx('tx2', expr1, expr2)
g1.addTx('tx3', expr2, expr1)
psiCtrl = g1.computePSI(g1.matchExpressions(g1._expressionCtrl))
psiCase = g1.computePSI(g1._expressionCase)
dpsi = psiCase - psiCtrl
assert dpsi.shape == (3, 4)
assert np.all(dpsi[:, 0] == [3 / 7 - .2, 3 / 7 - .2, 1 / 7 - .6])
assert np.all(dpsi[:, 1] == [4 / 11 - .3, 4 / 11 - .3, 3 / 11 - .4])
assert np.all(dpsi[:, 2] == pytest.approx([-.15, -.15, .3], .0001))
assert np.all(dpsi[:, 3] == pytest.approx([-.5, -.5, 1], .0001))
g2 = GeneExpression(txs, ctrl_ids, case_ids)
g2.addTx('tx1', expr1, expr2)
g2.addTx('tx2', expr1, expr2)
g2.addTx('tx3', expr2, expr1)
psiCtrl = g2.computePSI(g2.matchExpressions(g2._expressionCtrl))
psiCase = g2.computePSI(g2._expressionCase)
dpsi = psiCase - psiCtrl
assert dpsi.shape == (3, 4)
assert np.all(dpsi[:, 0] == [3 / 7 - .5, 3 / 7 - .5, 1 / 7 - .0])
assert np.all(dpsi[:, 1] == [4 / 11 - .4, 4 / 11 - .4, 3 / 11 - .2])
assert np.all(
dpsi[:, 2] == pytest.approx([1 / 4 - .35, 1 / 4 - .35, 1 / 2 -
.3], .0001))
assert np.all(dpsi[:,
3] == pytest.approx([0 - .35, 0 - .35, 1 - .3], .0001))
def test_computePSI():
expr = np.array([[2, 3, 4, 5]])
g = GeneExpression(txs, ctrl_ids, case_ids)
g.addTx('tx1', expr, expr)
psi = g.computePSI(g._expressionCtrl)
assert np.all(psi == np.array([[1, 1, 1, 1]]))
g.addTx('tx2', expr, expr)
psi = g.computePSI(g._expressionCtrl)
assert np.all(psi == np.array([[.5, .5, .5, .5], [.5, .5, .5, .5]]))
g.addTx('tx3', np.array([[6, 4, 2, 0]]), expr)
psi = g.computePSI(g._expressionCtrl)
assert np.all(
psi == np.array([[.2, .3, .4, .5], [.2, .3, .4, .5], [.6, .4, .2, 0]]))
def test_detectSwitches():
expression = np.array([[0, .5, 1, 2], [2, .05, .4, 5], [8, 3, .1, 0]])
dpsi = np.array([[1, -.5, .5, 0], [.5, -1, 1, 1], [-.3, 1, -.25, 0]])
wtdpsi = np.array([[0, 0, .15, .25, .05, .11, .09],
[0, 0, .15, .25, .05, .11, .09],
[0, 0, .15, .25, .05, .11, .09]])
g = GeneExpression(txs, ctrl_ids, case_ids)
g._storedTxs = ['tx1', 'tx2', 'tx3']
g._complete = True
g._matchedExpressionCtrl = expression
g._expressionCase = expression
g._wtdPSI = wtdpsi
g._dPSI = dpsi
g._wtdExp = np.array([0, .1, .2, .3, .4, .5, .6, .7, .8, .9, 1])
g._dExp = np.array([.94, .94, .96, .94])
switches = g.detectSwitches()
assert switches[('tx3', 'tx2')] == set('A')
assert switches[('tx1', 'tx3')] == set('Z')