Newick

Description

• http://evolution.genetics.washington.edu/phylip/newicktree.html
• http://en.wikipedia.org/wiki/Newick_format
• http://evolution.genetics.washington.edu/phylip/newick_doc.html

Reading

Schema-Specific Keyword Arguments

Supported Methods

Tree.get

(method reference)

tree = dendropy.Tree.get(
    path="tree.tre",
    schema="newick",
    label=None,
    taxon_namespace=None,
    collection_offset=None,
    tree_offset=None,
    rooting="default-unrooted",
    edge_length_type=float,
    suppress_edge_lengths=False,
    extract_comment_metadata=True,
    store_tree_weights=False,
    encode_splits=False,
    finish_node_fn=None,
    case_sensitive_taxon_labels=False,
    preserve_underscores=False,
    suppress_internal_node_taxa=True,
    suppress_leaf_node_taxa=False,
    terminating_semicolon_required=True,
    ignore_unrecognized_keyword_arguments=False,
    )

TreeList.get

(method reference)

tree_list = dendropy.TreeList.get(
    path="path/to/file",
    schema="newick",
    label=None,
    taxon_namespace=None,
    collection_offset=None,
    tree_offset=None,
    rooting="default-unrooted",
    edge_length_type=float,
    suppress_edge_lengths=False,
    extract_comment_metadata=True,
    store_tree_weights=False,
    encode_splits=False,
    finish_node_fn=None,
    case_sensitive_taxon_labels=False,
    preserve_underscores=False,
    suppress_internal_node_taxa=True,
    suppress_leaf_node_taxa=False,
    terminating_semicolon_required=True,
    ignore_unrecognized_keyword_arguments=False,
    )

TreeList.read

(method reference)

tree_list = dendropy.TreeList()
tree_list.read(
    path="path/to/file",
    schema="newick",
    collection_offset=None,
    tree_offset=None,
    rooting="default-unrooted",
    edge_length_type=float,
    suppress_edge_lengths=False,
    extract_comment_metadata=True,
    store_tree_weights=False,
    encode_splits=False,
    finish_node_fn=None,
    case_sensitive_taxon_labels=False,
    preserve_underscores=False,
    suppress_internal_node_taxa=True,
    suppress_leaf_node_taxa=False,
    terminating_semicolon_required=True,
    ignore_unrecognized_keyword_arguments=False,
    )

TreeArray.read

(method reference)

tree_array = dendropy.TreeArray()
tree_array.read(
    path="path/to/file",
    schema="newick",
    label=None,
    collection_offset=None,
    tree_offset=None,
    rooting="default-unrooted",
    edge_length_type=float,
    suppress_edge_lengths=False,
    extract_comment_metadata=True,
    store_tree_weights=False,
    encode_splits=False,
    finish_node_fn=None,
    case_sensitive_taxon_labels=False,
    preserve_underscores=False,
    suppress_internal_node_taxa=True,
    suppress_leaf_node_taxa=False,
    terminating_semicolon_required=True,
    ignore_unrecognized_keyword_arguments=False,
    )

DataSet.get

(method reference)

data_set = dendropy.DataSet.get(
    path="path/to/file",
    schema="newick",
    label=None,
    taxon_namespace=None,
    exclude_chars=False,
    exclude_trees=False,
    rooting="default-unrooted",
    edge_length_type=float,
    suppress_edge_lengths=False,
    extract_comment_metadata=True,
    store_tree_weights=False,
    encode_splits=False,
    finish_node_fn=None,
    case_sensitive_taxon_labels=False,
    preserve_underscores=False,
    suppress_internal_node_taxa=True,
    suppress_leaf_node_taxa=False,
    terminating_semicolon_required=True,
    ignore_unrecognized_keyword_arguments=False,
    )

DataSet.read

(method reference)

data_set = dendropy.DataSet()
data_set.read(
    path="path/to/file",
    schema="newick",
    exclude_chars=False,
    exclude_trees=False,
    rooting="default-unrooted",
    edge_length_type=float,
    suppress_edge_lengths=False,
    extract_comment_metadata=True,
    store_tree_weights=False,
    encode_splits=False,
    finish_node_fn=None,
    case_sensitive_taxon_labels=False,
    preserve_underscores=False,
    suppress_internal_node_taxa=True,
    suppress_leaf_node_taxa=False,
    terminating_semicolon_required=True,
    ignore_unrecognized_keyword_arguments=False,
    )

Writing

Schema-Specific Keyword Arguments

Supported Methods

Tree.write

(method reference)

d.write(
        path='outputfile.tre',
        schema='newick',
        suppress_leaf_taxon_labels=False,
        suppress_leaf_node_labels=True,
        suppress_internal_taxon_labels=False,
        suppress_internal_node_labels=False,
        suppress_rooting=False,
        suppress_edge_lengths=False,
        unquoted_underscores=False,
        preserve_spaces=False,
        store_tree_weights=False,
        taxon_token_map=None,
        suppress_annotations=True,
        annotations_as_nhx=False,
        suppress_item_comments=True,
        node_label_element_separator=' ',
        node_label_compose_fn=None,
        edge_label_compose_fn=None,
        real_value_format_specifier='',
        ignore_unrecognized_keyword_arguments=False,
        )

Tree.as_string

(method reference)

s = d.as_string(
        schema='newick',
        suppress_leaf_taxon_labels=False,
        suppress_leaf_node_labels=True,
        suppress_internal_taxon_labels=False,
        suppress_internal_node_labels=False,
        suppress_rooting=False,
        suppress_edge_lengths=False,
        unquoted_underscores=False,
        preserve_spaces=False,
        store_tree_weights=False,
        taxon_token_map=None,
        suppress_annotations=True,
        annotations_as_nhx=False,
        suppress_item_comments=True,
        node_label_element_separator=' ',
        node_label_compose_fn=None,
        edge_label_compose_fn=None,
        real_value_format_specifier='',
        ignore_unrecognized_keyword_arguments=False,
        )

TreeList.write

(method reference)

d.write(
        path='outputfile.tre',
        schema='newick',
        suppress_leaf_taxon_labels=False,
        suppress_leaf_node_labels=True,
        suppress_internal_taxon_labels=False,
        suppress_internal_node_labels=False,
        suppress_rooting=False,
        suppress_edge_lengths=False,
        unquoted_underscores=False,
        preserve_spaces=False,
        store_tree_weights=False,
        taxon_token_map=None,
        suppress_annotations=True,
        annotations_as_nhx=False,
        suppress_item_comments=True,
        node_label_element_separator=' ',
        node_label_compose_fn=None,
        edge_label_compose_fn=None,
        real_value_format_specifier='',
        ignore_unrecognized_keyword_arguments=False,
        )

TreeList.as_string

(method reference)

s = d.as_string(
        schema='newick',
        suppress_leaf_taxon_labels=False,
        suppress_leaf_node_labels=True,
        suppress_internal_taxon_labels=False,
        suppress_internal_node_labels=False,
        suppress_rooting=False,
        suppress_edge_lengths=False,
        unquoted_underscores=False,
        preserve_spaces=False,
        store_tree_weights=False,
        taxon_token_map=None,
        suppress_annotations=True,
        annotations_as_nhx=False,
        suppress_item_comments=True,
        node_label_element_separator=' ',
        node_label_compose_fn=None,
        edge_label_compose_fn=None,
        real_value_format_specifier='',
        ignore_unrecognized_keyword_arguments=False,
        )

DataSet.write

(method reference)

d.write(
        path='outputfile.tre',
        schema='newick',
        suppress_leaf_taxon_labels=False,
        suppress_leaf_node_labels=True,
        suppress_internal_taxon_labels=False,
        suppress_internal_node_labels=False,
        suppress_rooting=False,
        suppress_edge_lengths=False,
        unquoted_underscores=False,
        preserve_spaces=False,
        store_tree_weights=False,
        taxon_token_map=None,
        suppress_annotations=True,
        annotations_as_nhx=False,
        suppress_item_comments=True,
        node_label_element_separator=' ',
        node_label_compose_fn=None,
        edge_label_compose_fn=None,
        real_value_format_specifier='',
        ignore_unrecognized_keyword_arguments=False,
        )

DataSet.as_string

(method reference)

s = d.as_string(
        schema='newick',
        suppress_leaf_taxon_labels=False,
        suppress_leaf_node_labels=True,
        suppress_internal_taxon_labels=False,
        suppress_internal_node_labels=False,
        suppress_rooting=False,
        suppress_edge_lengths=False,
        unquoted_underscores=False,
        preserve_spaces=False,
        store_tree_weights=False,
        taxon_token_map=None,
        suppress_annotations=True,
        annotations_as_nhx=False,
        suppress_item_comments=True,
        node_label_element_separator=' ',
        node_label_compose_fn=None,
        edge_label_compose_fn=None,
        real_value_format_specifier='',
        ignore_unrecognized_keyword_arguments=False,
        )