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 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)