Python _validate_otu_ids_and_treeの例

コード例 #1

ファイル: test_util.py プロジェクト: shihuang047/scikit-bio

    def test_validate_otu_ids_and_tree(self):
        # basic valid input
        t = TreeNode.read(
            io.StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
                        '0.75,OTU5:0.75):1.25):0.0)root;'))
        counts = [1, 1, 1]
        otu_ids = ['OTU1', 'OTU2', 'OTU3']
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

        # all tips observed
        t = TreeNode.read(
            io.StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
                        '0.75,OTU5:0.75):1.25):0.0)root;'))
        counts = [1, 1, 1, 1, 1]
        otu_ids = ['OTU1', 'OTU2', 'OTU3', 'OTU4', 'OTU5']
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

        # no tips observed
        t = TreeNode.read(
            io.StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
                        '0.75,OTU5:0.75):1.25):0.0)root;'))
        counts = []
        otu_ids = []
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

        # all counts zero
        t = TreeNode.read(
            io.StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
                        '0.75,OTU5:0.75):1.25):0.0)root;'))
        counts = [0, 0, 0, 0, 0]
        otu_ids = ['OTU1', 'OTU2', 'OTU3', 'OTU4', 'OTU5']
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

コード例 #2

ファイル: _unifrac.py プロジェクト: ttimbers/scikit-bio

def _setup_multiple_unifrac(counts, otu_ids, tree, validate):
    if validate:
        _validate_otu_ids_and_tree(counts[0], otu_ids, tree)

    counts_by_node, tree_index, branch_lengths = _vectorize_counts_and_tree(counts, otu_ids, tree)

    return counts_by_node, tree_index, branch_lengths

コード例 #3

ファイル: test_util.py プロジェクト: ttimbers/scikit-bio

    def test_validate_otu_ids_and_tree(self):
        # basic valid input
        t = TreeNode.read(
            StringIO(u"(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:" u"0.75,OTU5:0.75):1.25):0.0)root;")
        )
        counts = [1, 1, 1]
        otu_ids = ["OTU1", "OTU2", "OTU3"]
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

        # all tips observed
        t = TreeNode.read(
            StringIO(u"(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:" u"0.75,OTU5:0.75):1.25):0.0)root;")
        )
        counts = [1, 1, 1, 1, 1]
        otu_ids = ["OTU1", "OTU2", "OTU3", "OTU4", "OTU5"]
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

        # no tips observed
        t = TreeNode.read(
            StringIO(u"(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:" u"0.75,OTU5:0.75):1.25):0.0)root;")
        )
        counts = []
        otu_ids = []
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

        # all counts zero
        t = TreeNode.read(
            StringIO(u"(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:" u"0.75,OTU5:0.75):1.25):0.0)root;")
        )
        counts = [0, 0, 0, 0, 0]
        otu_ids = ["OTU1", "OTU2", "OTU3", "OTU4", "OTU5"]
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

コード例 #4

ファイル: _unifrac.py プロジェクト: liupfskygre/scikit-bio

def _setup_multiple_unifrac(counts, otu_ids, tree, validate):
    if validate:
        _validate_otu_ids_and_tree(counts[0], otu_ids, tree)

    counts_by_node, tree_index, branch_lengths = \
        _vectorize_counts_and_tree(counts, otu_ids, tree)

    return counts_by_node, tree_index, branch_lengths

コード例 #5

ファイル: _faith_pd.py プロジェクト: RNAer/scikit-bio

def _setup_faith_pd(counts, otu_ids, tree, validate, single_sample):
    if validate:
        if single_sample:
            # only validate count if operating in single sample mode, they
            # will have already been validated otherwise
            counts = _validate_counts_vector(counts)
            _validate_otu_ids_and_tree(counts, otu_ids, tree)
        else:
            _validate_otu_ids_and_tree(counts[0], otu_ids, tree)

    counts_by_node, tree_index, branch_lengths = _vectorize_counts_and_tree(counts, otu_ids, tree)

    return counts_by_node, branch_lengths

コード例 #6

def _setup_faith_pd(counts, otu_ids, tree, validate, single_sample):
    if validate:
        if single_sample:
            # only validate count if operating in single sample mode, they
            # will have already been validated otherwise
            counts = _validate_counts_vector(counts)
            _validate_otu_ids_and_tree(counts, otu_ids, tree)
        else:
            _validate_otu_ids_and_tree(counts[0], otu_ids, tree)

    counts_by_node, tree_index, branch_lengths = \
        _vectorize_counts_and_tree(counts, otu_ids, tree)

    return counts_by_node, branch_lengths

コード例 #7

ファイル: test_util.py プロジェクト: RNAer/scikit-bio

    def test_validate_otu_ids_and_tree(self):
        # basic valid input
        t = TreeNode.read(
            io.StringIO(
                '(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
                '0.75,OTU5:0.75):1.25):0.0)root;'))
        counts = [1, 1, 1]
        otu_ids = ['OTU1', 'OTU2', 'OTU3']
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

        # all tips observed
        t = TreeNode.read(
            io.StringIO(
                '(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
                '0.75,OTU5:0.75):1.25):0.0)root;'))
        counts = [1, 1, 1, 1, 1]
        otu_ids = ['OTU1', 'OTU2', 'OTU3', 'OTU4', 'OTU5']
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

        # no tips observed
        t = TreeNode.read(
            io.StringIO(
                '(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
                '0.75,OTU5:0.75):1.25):0.0)root;'))
        counts = []
        otu_ids = []
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

        # all counts zero
        t = TreeNode.read(
            io.StringIO(
                '(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
                '0.75,OTU5:0.75):1.25):0.0)root;'))
        counts = [0, 0, 0, 0, 0]
        otu_ids = ['OTU1', 'OTU2', 'OTU3', 'OTU4', 'OTU5']
        self.assertTrue(_validate_otu_ids_and_tree(counts, otu_ids, t) is None)

コード例 #8

ファイル: _unifrac.py プロジェクト: liupfskygre/scikit-bio

def _validate(u_counts, v_counts, otu_ids, tree):
    _validate_counts_matrix([u_counts, v_counts], suppress_cast=True)
    _validate_otu_ids_and_tree(counts=u_counts, otu_ids=otu_ids, tree=tree)

コード例 #9

ファイル: _unifrac.py プロジェクト: ElDeveloper/biolopy

def _validate(u_counts, v_counts, otu_ids, tree):
    _validate_counts_matrix([u_counts, v_counts], suppress_cast=True)
    _validate_otu_ids_and_tree(counts=u_counts, otu_ids=otu_ids, tree=tree)