def testSeqid(self):
seqid = 0.50
label = "FSHB_BOVIN"
unique = uniqueSequences(FASTA, seqid)
refined = refineMSA(FASTA, seqid=seqid)
assert_array_equal(refined._getArray(), FASTA._getArray()[unique])
def testSeqid(self):
seqid = 0.50
label = 'FSHB_BOVIN'
unique = uniqueSequences(FASTA, seqid)
refined = refineMSA(FASTA, seqid=seqid)
assert_array_equal(refined._getArray(), FASTA._getArray()[unique])
def testSeqidLabel(self):
seqid = 0.50
label = 'FSHB_BOVIN'
labeled = refineMSA(FASTA, label=label)
unique = uniqueSequences(labeled, seqid)
unique[FASTA.getIndex(label)] = True
refined = refineMSA(FASTA, label=label, seqid=seqid)
assert_array_equal(refined._getArray(), labeled._getArray()[unique])
def testSeqidLabel(self):
seqid = 0.50
label = "FSHB_BOVIN"
labeled = refineMSA(FASTA, label=label)
unique = uniqueSequences(labeled, seqid)
unique[FASTA.getIndex(label)] = True
refined = refineMSA(FASTA, label=label, seqid=seqid)
assert_array_equal(refined._getArray(), labeled._getArray()[unique])
def testUnique2(self):
seqid = 0.5
unique = ones(FASTA_NUMBER, bool)
for i in range(FASTA_NUMBER):
if not unique[i]:
continue
for j in range(i + 1, FASTA_NUMBER):
if FASTA_EYE[i, j] >= seqid:
unique[j] = False
assert_array_equal(unique, uniqueSequences(FASTA, seqid))
def testUnique2(self):
seqid = 0.5
unique = ones(FASTA_NUMBER, bool)
for i in range(FASTA_NUMBER):
if not unique[i]:
continue
for j in range(i + 1, FASTA_NUMBER):
if FASTA_EYE[i, j] >= seqid:
unique[j] = False
assert_array_equal(unique, uniqueSequences(FASTA, seqid))
def testAll(self):
rowocc = 0.9
colocc = 0.9
seqid = 0.98
label = "FSHB_BOVIN"
refined = refineMSA(FASTA, label=label, seqid=seqid, rowocc=rowocc, colocc=colocc)
index = FASTA.getIndex(label)
which = FASTA_ALPHA[index].nonzero()[0]
expected = FASTA._getArray().take(which, 1)
expected = expected[uniqueSequences(expected, seqid)]
expected = expected[calcMSAOccupancy(expected, "row") >= rowocc]
which = (calcMSAOccupancy(expected) >= colocc).nonzero()[0]
expected = expected.take(which, 1)
assert_array_equal(refined._getArray(), expected)
def testAll(self):
rowocc = 0.9
colocc = 0.9
seqid = 0.98
label = 'FSHB_BOVIN'
refined = refineMSA(FASTA, label=label, seqid=seqid,
rowocc=rowocc, colocc=colocc)
index = FASTA.getIndex(label)
which = FASTA_ALPHA[index].nonzero()[0]
expected = FASTA._getArray().take(which, 1)
expected = expected[uniqueSequences(expected, seqid)]
expected = expected[calcMSAOccupancy(expected, 'row') >= rowocc]
which = (calcMSAOccupancy(expected) >= colocc).nonzero()[0]
expected = expected.take(which, 1)
assert_array_equal(refined._getArray(), expected)