Esempio n. 1
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    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])
Esempio n. 2
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    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])
Esempio n. 3
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    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])
Esempio n. 4
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    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])
Esempio n. 5
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    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))
Esempio n. 6
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    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))
Esempio n. 7
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    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)
Esempio n. 8
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    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)