NeXML

Description

Reading

Schema-Specific Keyword Arguments

NexmlReader.__init__(**kwargs)[source]
Keyword Arguments:

  • default_namespace (str) – Default namespace to use for elements.

  • case_sensitive_taxon_labels (boolean, default: False) – If True, then case is respected when matching taxon names. Default is False: case is ignored.

  • ignore_unrecognized_keyword_arguments (boolean, default: False) – If True, then unsupported or unrecognized keyword arguments will not result in an error. Default is False: unsupported keyword arguments will result in an error.

Supported Methods

Tree.get

(method reference)

tree = dendropy.Tree.get(
    path="path/to/file",
    schema="nexml",
    label=None,
    taxon_namespace=None,
    collection_offset=None,
    tree_offset=None,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

TreeList.get

(method reference)

tree_list = dendropy.TreeList.get(
    path="path/to/file",
    schema="nexml",
    label=None,
    taxon_namespace=None,
    collection_offset=None,
    tree_offset=None,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

TreeList.read

(method reference)

tree_list = dendropy.TreeList()
tree_list.read(
    path="path/to/file",
    schema="nexml",
    collection_offset=None,
    tree_offset=None,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

TreeArray.read

(method reference)

tree_array = dendropy.TreeArray()
tree_array.read(
    path="path/to/file",
    schema="nexml",
    collection_offset=None,
    tree_offset=None,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

DnaCharacterMatrix.get

(method reference)

chars = dendropy.DnaCharacterMatrix.get(
    path="path/to/file",
    schema="nexml",
    label=None,
    taxon_namespace=None,
    matrix_offset=None,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

RnaCharacterMatrix.get

(method reference)

chars = dendropy.RnaCharacterMatrix.get(
    path="path/to/file",
    schema="nexml",
    label=None,
    taxon_namespace=None,
    matrix_offset=None,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

ProteinCharacterMatrix.get

(method reference)

chars = dendropy.ProteinCharacterMatrix.get(
    path="path/to/file",
    schema="nexml",
    label=None,
    taxon_namespace=None,
    matrix_offset=None,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

RestrictionSitesCharacterMatrix.get

(method reference)

chars = dendropy.RestrictionSitesCharacterMatrix.get(
    path="path/to/file",
    schema="nexml",
    label=None,
    taxon_namespace=None,
    matrix_offset=None,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

InfiniteSitesCharacterMatrix.get

(method reference)

chars = dendropy.InfiniteSitesCharacterMatrix.get(
    path="path/to/file",
    schema="nexml",
    label=None,
    taxon_namespace=None,
    matrix_offset=None,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

StandardCharacterMatrix.get

(method reference)

chars = dendropy.StandardCharacterMatrix.get(
    path="path/to/file",
    schema="nexml",
    label=None,
    taxon_namespace=None,
    matrix_offset=None,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

DataSet.get

(method reference)

data_set = dendropy.DataSet.get(
    path="path/to/file",
    schema="nexus",
    label=None,
    taxon_namespace=None,
    exclude_chars=False,
    exclude_trees=False,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

DataSet.read

(method reference)

data_set = dendropy.DataSet()
data_set.read(
    path="path/to/file",
    schema="nexml",
    exclude_chars=False,
    exclude_trees=False,
    default_namespace="http://www.nexml.org/2009",
    case_sensitive_taxon_labels=False,
    ignore_unrecognized_keyword_arguments=False,
    )

Writing

Schema-Specific Keyword Arguments

NexmlWriter.__init__(**kwargs)[source]
Keyword Arguments:

  • markup_as_sequences (boolean) – If True, then character data will be marked up as sequences instead of individual cells. Defaults to False.

  • suppress_unreferenced_taxon_namespaces (boolean, default: False) – If True, then when writing DataSet objects, any TaxonNamespace object in the DataSet’s taxon_namespaces collection will not be written as a “TAXA” block if it is not referenced by any character matrix (char_matrices) or tree list (tree_lists).

  • ignore_unrecognized_keyword_arguments (boolean, default: False) – If True, then unsupported or unrecognized keyword arguments will not result in an error. Default is False: unsupported keyword arguments will result in an error.

Supported Methods

Tree.write

(method reference)

d.write(
        path='trees.xml',
        schema='nexml',
        ignore_unrecognized_keyword_arguments=False,
        )

Tree.as_string

(method reference)

s = d.as_string(
        schema='nexml',
        ignore_unrecognized_keyword_arguments=False,
        )

TreeList.write

(method reference)

d.write(
        path='trees.xml',
        schema='nexml',
        ignore_unrecognized_keyword_arguments=False,
        )

TreeList.as_string

(method reference)

s = d.as_string(
        schema='nexml',
        ignore_unrecognized_keyword_arguments=False,
        )

DnaCharacterMatrix.write

(method reference)

d.write(
        path='data.xml',
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

DnaCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

RnaCharacterMatrix.write

(method reference)

d.write(
        path='data.xml',
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

RnaCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

ProteinCharacterMatrix.write

(method reference)

d.write(
        path='data.xml',
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

ProteinCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

RestrictionSitesCharacterMatrix.write

(method reference)

d.write(
        path='data.xml',
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

RestrictionSitesCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

InfiniteSitesCharacterMatrix.write

(method reference)

d.write(
        path='data.xml',
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

InfiniteSitesCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

StandardCharacterMatrix.write

(method reference)

d.write(
        path='data.xml',
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

StandardCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema='nexml',
        markup_as_sequences=False,
        ignore_unrecognized_keyword_arguments=False,
        )

DataSet.write

(method reference)

d.write(
        path='data.xml',
        schema='nexml',
        markup_as_sequences=False,
        suppress_unreferenced_taxon_namespaces=False,
        ignore_unrecognized_keyword_arguments=False,
        )

DataSet.as_string

(method reference)

s = d.as_string(
        schema='nexml',
        markup_as_sequences=False,
        suppress_unreferenced_taxon_namespaces=False,
        ignore_unrecognized_keyword_arguments=False,
        )