Пример #1
0
def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree_string = Newick.daylight_example_tree
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.IntegerInterval(
                'first_index', 'last_index',
                'eigenfunction index range (1 means Fiedler)',
                0, 12, low=0),
            Form.CheckGroup('check_options', 'output options', [
                Form.CheckItem('reflect_trees', 'reflect trees', True),
                Form.CheckItem('draw_background', 'draw background', True),
                Form.CheckItem('draw_labels', 'draw labels', True)]),
            Form.Integer('width', 'physical width', 880, low=10, high=1000),
            Form.Integer('height', 'physical height', 680, low=10, high=1000),
            Form.Integer('inner_margin', 'inner margin', 10, low=0, high=1000),
            Form.Integer('outer_margin', 'outer margin', 0, low=0, high=1000),
            Form.ImageFormat()]
    return form_objects
Пример #2
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree = Newick.parse(g_tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the default tip data lines
    default_tip_data_lines = [
            'a : A',
            'b : A',
            'c : C',
            'd : T',
            'e : T',
            'f : T']
    # define the default rate matrix lines
    R = np.array([
        [-1, 1/3.0, 1/3.0, 1/3.0],
        [1/3.0, -1, 1/3.0, 1/3.0],
        [1/3.0, 1/3.0, -1, 1/3.0],
        [1/3.0, 1/3.0, 1/3.0, -1]])
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.MultiLine('column', 'tip data',
                '\n'.join(default_tip_data_lines)),
            Form.Matrix('matrix', 'rate matrix',
                R, MatrixUtil.assert_rate_matrix),
            Form.ImageFormat()]
    return form_objects
Пример #3
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def get_form():
    """
    @return: the body of a form
    """
    # define the default tree string
    tree_string = Newick.brown_example_tree
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the default alignment string
    default_alignment_string = Fasta.brown_example_alignment.strip()
    # define the default nucleotide distribution weights
    default_nt_lines = [
            'A : 1',
            'C : 1',
            'G : 1',
            'T : 1']
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.MultiLine('alignment', 'nucleotide alignment',
                default_alignment_string),
            Form.MultiLine('weights', 'nucleotide weights',
                '\n'.join(default_nt_lines)),
            Form.Float('kappa', 'transition transversion rate ratio',
                2, low_inclusive=0)]
    return form_objects
Пример #4
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree_string = Newick.daylight_example_tree
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.IntegerInterval(
                'first_index', 'last_index',
                'eigenfunction index range (1 means Fiedler)',
                0, 12, low=0),
            Form.CheckGroup('check_options', 'output options', [
                Form.CheckItem('reflect_trees',
                    'reflect trees across the vertical axis'),
                Form.CheckItem('show_subfigure_labels',
                    'show subfigure labels', True),
                Form.CheckItem('show_vertex_labels',
                    'show vertex labels')]),
            Form.Float('width', 'width (centimeters)',
                12, low_inclusive=1, high_exclusive=1000),
            Form.Float('height', 'height (centimeters)',
                8, low_inclusive=1, high_exclusive=1000),
            Form.Float('inner_margin', 'inner margin (centimeters)',
                0.25, low_inclusive=0, high_exclusive=1000),
            Form.RadioGroup('radio_options', 'tree layout options', [
                Form.RadioItem('equal_daylight_layout',
                    'equal daylight layout', True),
                Form.RadioItem('equal_arc_layout',
                    'equal arc layout')]),
            Form.TikzFormat()]
    return form_objects
Пример #5
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.Integer('ncols', 'sample this many nucleotide columns',
                100, low=1, high=1000),
            Form.MultiLine('frequency_a', 'first component frequencies',
                get_frequency_string(0)),
            Form.Float('kappa_a', 'first component kappa',
                get_kappa(0), low_inclusive=0),
            Form.Float('weight_a', 'first component weight',
                get_weight(0), low_inclusive=0),
            Form.MultiLine('frequency_b', 'second component frequencies',
                get_frequency_string(1)),
            Form.Float('kappa_b', 'second component kappa',
                get_kappa(1), low_inclusive=0),
            Form.Float('weight_b', 'second component weight',
                get_weight(1), low_inclusive=0),
            Form.RadioGroup('fmt', 'output format options', [
                Form.RadioItem('fasta', 'fasta'),
                Form.RadioItem('nex', 'nexus', True)])]
    return form_objects
Пример #6
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree',
                formatted_tree_string),
            Form.MultiLine('alignment', 'nucleotide alignment',
                g_sample_alignment_string.strip()),
            Form.Matrix('matrix_a', 'first nucleotide rate matrix',
                g_nt_matrix_a),
            Form.Float('weight_a', 'first mixture weight',
                1, low_inclusive=0),
            Form.Matrix('matrix_b', 'second nucleotide rate matrix',
                g_nt_matrix_b),
            Form.Float('weight_b', 'second mixture weight',
                2, low_inclusive=0),
            Form.Matrix('matrix_c', 'third nucleotide rate matrix',
                g_nt_matrix_c),
            Form.Float('weight_c', 'third mixture weight',
                3, low_inclusive=0)]
    return form_objects
Пример #7
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def get_form():
    """
    @return: a list of form objects
    """
    # reformat the tree string
    tree = Newick.parse(g_tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 75)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree_string', 'newick tree',
                formatted_tree_string),
            Form.Float('scaling_factor',
                'figure scaling factor', 3.0, low_exclusive=0),
            Form.RadioGroup('label_mode', 'label mode', [
                Form.RadioItem('label_mode_suppressed',
                    'suppress all vertex labels', True),
                Form.RadioItem('label_mode_leaf_only',
                    'draw leaf names'),
                Form.RadioItem('label_mode_show',
                    'draw arbitrary short names at all vertices')]),
            Form.RadioGroup('sanitization_options',
                'taxon label sanitization options', [
                    Form.RadioItem('no_sanitization',
                        'allow TikZ to interpret the taxon labels', True),
                    Form.RadioItem('sanitization',
                        'attempt an ad-hoc sanitization of taxon labels')]),
            Form.RadioGroup('tree_layout', 'tree layout options', [
                Form.RadioItem('equal_arc', 'equal arc layout', True),
                Form.RadioItem('equal_daylight', 'equal daylight layout')]),
            Form.LatexFormat()]
    return form_objects
Пример #8
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree_string = '((((a:5)a:5, (b:5)b:5)A:1.5)A:1.5, (((c:5)c:5, (d:5)d:5)B:1.5)B:1.5);'
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    return [Form.MultiLine('tree', 'newick tree', formatted_tree_string)]
Пример #9
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree_string = Newick.daylight_example_tree
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    return [Form.MultiLine('tree', 'newick tree', formatted_tree_string)]
Пример #10
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def get_response_content(fs):
    # Read the newick trees.
    true_tree = Newick.parse(fs.true_tree, Newick.NewickTree)
    test_tree = Newick.parse(fs.test_tree, Newick.NewickTree)
    flags = get_flags(fs)
    # Get a list of maps from node id to harmonic extension.
    true_tree_leaf_ids = set(id(x) for x in true_tree.gen_tips())
    nleaves = len(true_tree_leaf_ids)
    id_to_full_val_list = [
        Harmonic.get_harmonic_valuations(true_tree, i)
        for i in range(1, nleaves)
    ]
    id_map = get_true_leaf_id_to_test_leaf_id(true_tree, test_tree)
    test_id_to_adj = get_id_to_adj(test_tree)
    test_id_to_name = get_id_to_name(test_tree)
    # Get the list of id to val maps with respect to leaf ids of the test tree.
    test_tree_internal_ids = set(id(x) for x in test_tree.gen_internal_nodes())
    test_tree_leaf_ids = set(id(x) for x in test_tree.gen_tips())
    id_to_val_list = []
    for id_to_full_val in id_to_full_val_list:
        d = {}
        for x in true_tree_leaf_ids:
            value = id_to_full_val[x]
            if abs(value) < 1e-8:
                raise ValueError('the true tree is too symmetric')
            elif value < 0:
                s = -1
            else:
                s = 1
            d[id_map[x]] = s
        for x in test_tree_internal_ids:
            d[x] = None
        id_to_val_list.append(d)
    # Attempt to find a sign assignment.
    id_to_vals = SeekEigenLacing.rec_eigen(test_id_to_adj, id_to_val_list,
                                           flags)
    # Reorder the leaf and the internal node ids according to name order.
    leaf_pair = sorted((test_id_to_name[x], x) for x in test_tree_leaf_ids)
    internal_pair = sorted(
        (test_id_to_name[x], x) for x in test_tree_internal_ids)
    reordered_leaf_ids = zip(*leaf_pair)[1]
    reordered_internal_ids = zip(*internal_pair)[1]
    # Check for a failure to find a certificate.
    if not id_to_vals:
        return 'no non-rejection certificate was found'
    # Start writing the response.
    out = StringIO()
    print >> out, 'leaf sign valuations:'
    for x in reordered_leaf_ids:
        print >> out, test_id_to_name[x], get_sign_string(id_to_vals[x])
    print >> out
    print >> out, 'vertex sign compatible internal vertex valuations:'
    for x in reordered_internal_ids:
        print >> out, test_id_to_name[x], get_sign_string(id_to_vals[x])
    return out.getvalue()
Пример #11
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def get_form():
    """
    @return: the body of a form
    """
    # format the default tree string
    tree = Newick.parse(g_default_tree, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'tree', formatted_tree_string)]
    return form_objects
Пример #12
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def get_response_content(fs):
    # Read the newick trees.
    true_tree = Newick.parse(fs.true_tree, Newick.NewickTree)
    test_tree = Newick.parse(fs.test_tree, Newick.NewickTree)
    flags = get_flags(fs)
    # Get a list of maps from node id to harmonic extension.
    true_tree_leaf_ids = set(id(x) for x in true_tree.gen_tips())
    nleaves = len(true_tree_leaf_ids)
    id_to_full_val_list = [Harmonic.get_harmonic_valuations(
        true_tree, i) for i in range(1, nleaves)]
    id_map =  get_true_leaf_id_to_test_leaf_id(true_tree, test_tree)
    test_id_to_adj = get_id_to_adj(test_tree)
    test_id_to_name = get_id_to_name(test_tree)
    # Get the list of id to val maps with respect to leaf ids of the test tree.
    test_tree_internal_ids = set(id(x) for x in test_tree.gen_internal_nodes())
    test_tree_leaf_ids = set(id(x) for x in test_tree.gen_tips())
    id_to_val_list = []
    for id_to_full_val in id_to_full_val_list:
        d = {}
        for x in true_tree_leaf_ids:
            value = id_to_full_val[x]
            if abs(value) < 1e-8:
                raise ValueError('the true tree is too symmetric')
            elif value < 0:
                s = -1
            else:
                s = 1
            d[id_map[x]] = s
        for x in test_tree_internal_ids:
            d[x] = None
        id_to_val_list.append(d)
    # Attempt to find a sign assignment.
    id_to_vals = SeekEigenLacing.rec_eigen(
            test_id_to_adj, id_to_val_list, flags)
    # Reorder the leaf and the internal node ids according to name order.
    leaf_pair = sorted(
            (test_id_to_name[x], x) for x in test_tree_leaf_ids)
    internal_pair = sorted(
            (test_id_to_name[x], x) for x in test_tree_internal_ids)
    reordered_leaf_ids = zip(*leaf_pair)[1]
    reordered_internal_ids = zip(*internal_pair)[1]
    # Check for a failure to find a certificate.
    if not id_to_vals:
        return 'no non-rejection certificate was found'
    # Start writing the response.
    out = StringIO()
    print >> out, 'leaf sign valuations:'
    for x in reordered_leaf_ids:
        print >> out, test_id_to_name[x], get_sign_string(id_to_vals[x])
    print >> out
    print >> out, 'vertex sign compatible internal vertex valuations:'
    for x in reordered_internal_ids:
        print >> out, test_id_to_name[x], get_sign_string(id_to_vals[x])
    return out.getvalue()
Пример #13
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def get_form():
    """
    @return: a list of form objects
    """
    # reformat the tree string
    tree = Newick.parse(g_tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 75)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree_string', 'newick tree',
                formatted_tree_string)]
    return form_objects
Пример #14
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def get_form():
    """
    @return: the body of a form
    """
    # format the default tree string
    tree = Newick.parse(g_default_tree, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'tree', formatted_tree_string),
            Form.SingleLine('vertex',
                'distinguished vertex of articulation', 'r')]
    return form_objects
Пример #15
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.Float('sf', 'scaling factor', 0.333333, low_exclusive=0)]
    return form_objects
Пример #16
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree_string = stone_example_tree
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.SingleLine('node', 'the name of the node to remove', 'a')]
    return form_objects
Пример #17
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree_string = Newick.daylight_example_tree
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.Integer('segments',
                'minimum segment count', 200, low=1, high=10000)]
    return form_objects
Пример #18
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def get_form():
    """
    @return: the body of a form
    """
    # define the newick string and the ordered labels
    tree = Newick.parse(g_default_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    labels = list('xyabcmnp')
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.MultiLine('order', 'sequence order', '\n'.join(labels)),
            Form.Integer('length', 'sequence length', 60, low=2)]
    return form_objects
Пример #19
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree and alignment strings
    tree_string = '(((Human:0.1, Chimpanzee:0.2)to-chimp:0.8, Gorilla:0.3)to-gorilla:0.7, Orangutan:0.4, Gibbon:0.5)all;'
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    alignment_string = Fasta.brown_example_alignment.strip()
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.MultiLine('fasta', 'fasta alignment', alignment_string)]
    return form_objects
Пример #20
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def get_form():
    """
    @return: the body of a form
    """
    # define the tree and alignment strings
    tree_string = Newick.brown_example_tree
    tree = Newick.parse(tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    alignment_string = Fasta.brown_example_alignment.strip()
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.MultiLine('fasta', 'fasta alignment', alignment_string)]
    return form_objects
Пример #21
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def get_response_content(fs):
    # get the tree
    tree = Newick.parse(fs.tree, Newick.NewickTree)
    tree.assert_valid()
    # get the mixture weights
    weights = [fs.weight_a, fs.weight_b, fs.weight_c]
    # get the matrices
    matrices = [fs.matrix_a, fs.matrix_b, fs.matrix_c]
    for R in matrices:
        if R.shape != (4,4):
            msg = 'expected each nucleotide rate matrix to be 4x4'
            raise HandlingError(msg)
    # get the nucleotide alignment
    try:
        alignment = Fasta.Alignment(fs.alignment.splitlines())
        alignment.force_nucleotide()
    except Fasta.AlignmentError as e:
        raise HandlingError(e)
    # create the mixture proportions
    weight_sum = sum(weights)
    mixture_proportions = [weight / weight_sum for weight in weights]
    # create the rate matrix objects
    ordered_states = list('ACGT')
    rate_matrix_objects = []
    for R in matrices:
        rate_matrix_object = RateMatrix.RateMatrix(R.tolist(), ordered_states)
        rate_matrix_objects.append(rate_matrix_object)
    # create the mixture model
    mixture_model = SubModel.MixtureModel(mixture_proportions,
            rate_matrix_objects)
    # normalize the mixture model
    mixture_model.normalize()
    # return the html string
    return do_analysis(mixture_model, alignment, tree) + '\n'
Пример #22
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def main():
    # create the alignment object
    print 'creating the alignment...'
    alignment_string = Fasta.brown_example_alignment.strip()
    alignment = Fasta.Alignment(StringIO(alignment_string))
    # create a tree object
    print 'creating the tree...'
    tree_string = Newick.brown_example_tree
    tree = Newick.parse(tree_string, Newick.NewickTree)
    # create a rate matrix object
    print 'creating the rate matrix object...'
    distribution = {'A': .25, 'C': .25, 'G': .25, 'T': .25}
    kappa = 2.0
    row_major_rate_matrix = RateMatrix.get_unscaled_hky85_rate_matrix(
            distribution, kappa).get_row_major_rate_matrix()
    rate_matrix = RateMatrix.FastRateMatrix(
            row_major_rate_matrix, list('ACGT'))
    rate_matrix.normalize()
    # get the mle_rates
    print 'getting the mle rates...'
    mle_rates = get_mle_rates(tree, alignment, rate_matrix)
    print 'mle rates:'
    print mle_rates
    print 'stockholm string:'
    print get_stockholm_string(tree, alignment, mle_rates)
Пример #23
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def main():
    import EqualArcLayout
    import Newick
    import SpatialTree
    # make a spatial tree
    tree = Newick.parse(Newick.daylight_example_tree, SpatialTree.SpatialTree)
    EqualArcLayout.do_layout(tree)
    max_size = (640, 480)
    image_formats = ('png', 'pdf', 'ps', 'svg')
    for image_format in image_formats:
        # get the image string
        image_string = get_tree_image(tree, max_size, image_format)
        # write the image file
        image_filename = 'test.%s' % image_format
        with open(image_filename, 'wb') as fout:
            fout.write(image_string)
        print 'created', image_filename
    # write an html file
    html_filename = 'test.html'
    with open(html_filename, 'w') as fout:
        print >> fout, '<html><body>'
        for image_format in image_formats:
            image_filename = 'test.%s' % image_format
            print >> fout, '<a href="%s">%s</a><br/>' % (
                    image_filename, image_filename)
        print >> fout, '</body></html>'
    print 'created', html_filename
Пример #24
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 def process_line(self, line):
     """
     Possibly add an attribute.
     The attribute can be a floating point value or a newick tree.
     """
     self.processed_lines.append(line)
     arr = [x.strip() for x in line.split('=')]
     if len(arr) > 1:
         var, value = arr[0], arr[-1]
         var_arr = var.split()
         # read the log likelihood
         if var == 'Log Likelihood' and value.endswith(';'):
             try:
                 fvalue = float(value[:-1])
                 setattr(self, 'lnL', fvalue)
                 return
             except ValueError:
                 pass
         # read a tree assignment
         if len(var_arr) == 2 and var_arr[0] == 'Tree':
             treename = var_arr[1]
             tree_string = value
             tree = Newick.parse(tree_string, Newick.NewickTree)
             setattr(self, treename, tree)
             return
         # read a standard variable assignment
         if len(var_arr) == 1:
             try:
                 fvalue = float(value)
                 setattr(self, var, fvalue)
                 return
             except ValueError:
                 pass
Пример #25
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def get_response_content(fs):
    # get the tree
    tree = Newick.parse(fs.tree, Newick.NewickTree)
    tree.assert_valid()
    # get the set of names
    selection = Util.get_stripped_lines(fs.names.splitlines())
    selected_name_set = set(selection)
    possible_name_set = set(node.get_name() for node in tree.gen_tips())
    extra_names = selected_name_set - possible_name_set
    if extra_names:
        msg_a = 'the following selected names '
        msg_b = 'are not valid tips: ' + ', '.join(extra_names)
        raise HandlingError(msg_a + msg_b)
    # get the list of tip nodes to remove
    if fs.remove:
        nodes_to_remove = [
                node for node in tree.gen_tips() if node.name in selection]
    elif fs.keep:
        nodes_to_remove = [
                node for node in tree.gen_tips() if node.name not in selection]
    # prune the tree
    for node in nodes_to_remove:
        tree.prune(node)
    # merge segmented branches
    internal_nodes_to_remove = [
            node for node in tree.preorder() if node.get_child_count() == 1]
    for node in internal_nodes_to_remove:
        tree.remove_node(node)
    # return the response
    return tree.get_newick_string() + '\n'
Пример #26
0
 def __call__(self, X_logs):
     """
     The vth entry of X corresponds to the log rate of the branch above v.
     Return the quantity to be minimized (the neg log likelihood).
     @param X: vector of branch rate logs
     @return: negative log likelihood
     """
     X = [math.exp(x) for x in X_logs]
     B_subs = {}
     for v_parent, v_child in self.R:
         edge = frozenset([v_parent, v_child])
         r = X[v_child]
         t = self.B[edge]
         B_subs[edge] = r * t
     newick_string = FtreeIO.RBN_to_newick(self.R, B_subs, self.N_leaves)
     tree = Newick.parse(newick_string, Newick.NewickTree)
     # define the rate matrix object; horrible
     dictionary_rate_matrix = RateMatrix.get_jukes_cantor_rate_matrix() 
     ordered_states = list('ACGT') 
     row_major_rate_matrix = MatrixUtil.dict_to_row_major(
             dictionary_rate_matrix, ordered_states, ordered_states)
     rate_matrix_object = RateMatrix.RateMatrix(
             row_major_rate_matrix, ordered_states) 
     # get the log likelihood
     ll = PhyLikelihood.get_log_likelihood(
             tree, self.alignment, rate_matrix_object)
     return -ll
Пример #27
0
def get_response_content(fs):
    """
    @param fs: a FieldStorage object containing the cgi arguments
    @return: a (response_headers, response_text) pair
    """
    # get the tree
    tree = Newick.parse(fs.tree, Newick.NewickTree)
    tree.assert_valid()
    # find nodes with a branch length of zero
    zero_blen_nodes = [node for node in tree.preorder() if node.blen == 0.0]
    # deal with these nodes appropriately
    for node in zero_blen_nodes:
        if node.blen != 0.0:
            # it is possible that this node no longer has branch length zero
            continue
        elif node.has_children():
            # remove internal nodes with zero branch length
            tree.remove_node(node)
        else:
            # prune terminal nodes with zero branch length
            intersection = tree.prune(node)
            # remove intersection nodes that have a single child
            if intersection.get_child_count() == 1:
                tree.remove_node(intersection)
    # return the response
    return tree.get_newick_string() + '\n'
Пример #28
0
def get_form():
    """
    @return: the body of a form
    """
    # define the tree string
    tree = Newick.parse(g_tree_string, Newick.NewickTree)
    formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
    # define the form objects
    form_objects = [
            Form.MultiLine('tree', 'newick tree', formatted_tree_string),
            Form.Float('width', 'width (centimeters)',
                12, low_inclusive=1, high_exclusive=1000),
            Form.Float('height', 'height (centimeters)',
                8, low_inclusive=1, high_exclusive=1000),
            Form.TikzFormat()]
    return form_objects
Пример #29
0
def get_response_content(fs):
    # get a properly formatted newick tree with branch lengths
    tree_string = '((1:1, 2:1)6:1, 3:1, (4:1, 5:1)7:1)8;'
    tree = Newick.parse(tree_string, SpatialTree.SpatialTree)
    # get the fiedler-like vertex valuation
    fiedler = [1, 1, -1, -1, -1, 1, -1, -1]
    # create a node id map
    ids = [None]*8
    for node in tree.preorder():
        index = int(node.name) - 1
        ids[index] = id(node)
    # convert fiedler into a dictionary
    v1 = dict((ids[i], float(fiedler[i])) for i in range(8))
    # convert the annotations into dictionaries
    v2s = [dict((ids[i], float(v[i])) for i in range(8)) for v in g_annotation]
    # do the layout
    try:
        layout = FastDaylightLayout.StraightBranchLayout()
        layout.do_layout(tree)
    except RuntimeError as e:
        pass
    # draw the image
    try:
        ext = Form.g_imageformat_to_ext[fs.imageformat]
        return DrawEigenLacing.get_eg2_image(
                tree, (640, 480), ext,
                v1, v2s,
                fs.draw_background, fs.draw_vertices, fs.draw_labels)
    except CairoUtil.CairoUtilError as e:
        raise HandlingError(e)
Пример #30
0
def get_tikz_lines(newick, eigenvector_index, yaw, pitch):
    """
    @param eigenvector_index: 1 is Fiedler
    """
    tree = Newick.parse(newick, SpatialTree.SpatialTree) 
    # change the node names and get the new tree string
    for node in tree.preorder():
        node.name = 'n' + str(id(node))
    newick = NewickIO.get_newick_string(tree)
    # do the layout
    layout = FastDaylightLayout.StraightBranchLayout() 
    layout.do_layout(tree) 
    tree.fit((g_xy_scale, g_xy_scale))
    name_to_location = dict((
        x.name, tree._layout_to_display(x.location)) for x in tree.preorder())
    T, B, N = FtreeIO.newick_to_TBN(newick)
    # get some vertices
    leaves = Ftree.T_to_leaves(T)
    internal = Ftree.T_to_internal_vertices(T)
    vertices = leaves + internal
    # get the locations
    v_to_location = dict((v, name_to_location[N[v]]) for v in vertices)
    # get the valuations
    w, V = Ftree.TB_to_harmonic_extension(T, B, leaves, internal)
    index_to_val = V[:, eigenvector_index-1]
    v_to_val = dict(
            (vertices[i], g_z_scale*val) for i, val in enumerate(index_to_val))
    # get the coordinates
    v_to_xyz = get_v_to_xyz(yaw, v_to_location, v_to_val)
    # add intersection vertices
    add_intersection_vertices(T, B, v_to_xyz)
    intersection_vertices = sorted(v for v in v_to_xyz if v not in vertices)
    # get lines of the tikz file
    return xyz_to_tikz_lines(T, B, pitch, v_to_xyz,
            leaves, internal, intersection_vertices)
Пример #31
0
def make_file(newick_string, filename_prefix, iterations, min_segments):
    import DrawTreeImage
    import Newick
    import SpatialTree
    # make a spatial tree
    tree = Newick.parse(newick_string, SpatialTree.SpatialTree)
    # break the tree into pieces
    segment_tree(tree, min_segments, SpatialTree.SpatialTreeNode)
    print 'broke the tree into', sum(1 for node in tree.preorder()), 'nodes'
    # do the layout
    do_layout(tree, iterations)
    print 'did the layout'
    # color some of the branches
    red = 'ff0000'
    green = '00ff00'
    blue = '0000ff'
    for child, color in zip(tree.root.children, (red, green, blue)):
        for node in child.preorder():
            node.branch_color = color
    # get the image string
    image_format = 'png'
    image_string = DrawTreeImage.get_tree_image(tree, (640, 480), image_format)
    print 'created the image string'
    # write the image file
    with open('%s.%s' % (filename_prefix, image_format), 'wb') as fout:
        fout.write(image_string)