.venv_haddock/lib/python3.12/site-packages/Bio/Phylo/NeXMLIO.py

# Copyright (C) 2013 by Ben Morris (ben@bendmorris.com)
# Based on Bio.Nexus, copyright 2005-2008 by Frank Kauff & Cymon J. Cox
# and Bio.Phylo.Newick, copyright 2009 by Eric Talevich.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""I/O function wrappers for the NeXML file format.

See: http://www.nexml.org
"""

from io import StringIO
from xml.dom import minidom
from xml.etree import ElementTree

from Bio.Phylo import NeXML

from ._cdao_owl import cdao_elements
from ._cdao_owl import cdao_namespaces
from ._cdao_owl import resolve_uri

NAMESPACES = {
    "xsi": "http://www.w3.org/2001/XMLSchema-instance",
    "xml": "http://www.w3.org/XML/1998/namespace",
    "nex": "http://www.nexml.org/2009",
    "xsd": "http://www.w3.org/2001/XMLSchema#",
}
NAMESPACES.update(cdao_namespaces)
DEFAULT_NAMESPACE = NAMESPACES["nex"]
VERSION = "0.9"
SCHEMA = "http://www.nexml.org/2009/nexml/xsd/nexml.xsd"

register_namespace = ElementTree.register_namespace

for prefix, uri in NAMESPACES.items():
    register_namespace(prefix, uri)


def qUri(s):
    """Given a prefixed URI, return the full URI."""
    return resolve_uri(s, namespaces=NAMESPACES, xml_style=True)


def cdao_to_obo(s):
    """Optionally converts a CDAO-prefixed URI into an OBO-prefixed URI."""
    return f"obo:{cdao_elements[s[len('cdao:') :]]}"


def matches(s):
    """Check for matches in both CDAO and OBO namespaces."""
    if s.startswith("cdao:"):
        return (s, cdao_to_obo(s))
    else:
        return (s,)


class NeXMLError(Exception):
    """Exception raised when NeXML object construction cannot continue."""


# ---------------------------------------------------------
# Public API


def parse(handle, **kwargs):
    """Iterate over the trees in a NeXML file handle.

    :returns: generator of Bio.Phylo.NeXML.Tree objects.

    """
    return Parser(handle).parse(**kwargs)


def write(trees, handle, plain=False, **kwargs):
    """Write a trees in NeXML format to the given file handle.

    :returns: number of trees written.

    """
    return Writer(trees).write(handle, plain=plain, **kwargs)


# ---------------------------------------------------------
# Input


class Parser:
    """Parse a NeXML tree given a file handle.

    Based on the parser in ``Bio.Nexus.Trees``.
    """

    def __init__(self, handle):
        """Initialize parameters for NeXML file parser."""
        self.handle = handle

    @classmethod
    def from_string(cls, treetext):
        """Convert file handle to StringIO object."""
        handle = StringIO(treetext)
        return cls(handle)

    def add_annotation(self, node_dict, meta_node):
        """Add annotations for the NeXML parser."""
        if "property" in meta_node.attrib:
            prop = meta_node.attrib["property"]
        else:
            prop = "meta"

        if prop in matches("cdao:has_Support_Value"):
            node_dict["confidence"] = float(meta_node.text)
        else:
            node_dict[prop] = meta_node.text

    def parse(self, values_are_confidence=False, rooted=False):
        """Parse the text stream this object was initialized with."""
        nexml_doc = ElementTree.iterparse(self.handle, events=("end",))

        for event, node in nexml_doc:
            if node.tag == qUri("nex:tree"):
                node_dict = {}
                node_children = {}
                root = None

                nodes = []
                edges = []
                for child in node:
                    if child.tag == qUri("nex:node"):
                        nodes.append(child)
                    if child.tag == qUri("nex:edge"):
                        edges.append(child)

                for node in nodes:
                    node_id = node.attrib["id"]
                    this_node = node_dict[node_id] = {}
                    if "otu" in node.attrib and node.attrib["otu"]:
                        this_node["name"] = node.attrib["otu"]
                    if "root" in node.attrib and node.attrib["root"] == "true":
                        root = node_id

                    for child in node:
                        if child.tag == qUri("nex:meta"):
                            self.add_annotation(node_dict[node_id], child)

                srcs = set()
                tars = set()
                for edge in edges:
                    src, tar = edge.attrib["source"], edge.attrib["target"]
                    srcs.add(src)
                    tars.add(tar)
                    if src not in node_children:
                        node_children[src] = set()

                    node_children[src].add(tar)
                    if "length" in edge.attrib:
                        node_dict[tar]["branch_length"] = float(edge.attrib["length"])
                    if "property" in edge.attrib and edge.attrib["property"] in matches(
                        "cdao:has_Support_Value"
                    ):
                        node_dict[tar]["confidence"] = float(edge.attrib["content"])

                    for child in edge:
                        if child.tag == qUri("nex:meta"):
                            self.add_annotation(node_dict[tar], child)

                if root is None:
                    # if no root specified, start the recursive tree creation function
                    # with the first node that's not a child of any other nodes
                    rooted = False
                    possible_roots = (
                        node.attrib["id"]
                        for node in nodes
                        if node.attrib["id"] in srcs and node.attrib["id"] not in tars
                    )
                    root = next(possible_roots)
                else:
                    rooted = True

                yield NeXML.Tree(
                    root=self._make_tree(root, node_dict, node_children), rooted=rooted
                )

    @classmethod
    def _make_tree(cls, node, node_dict, children):
        """Traverse the tree creating a nested clade structure (PRIVATE).

        Return a NeXML.Clade, and calls itself recursively for each child,
        traversing the  entire tree and creating a nested structure of NeXML.Clade
        objects.
        """
        this_node = node_dict[node]
        clade = NeXML.Clade(**this_node)

        if node in children:
            clade.clades = [
                cls._make_tree(child, node_dict, children) for child in children[node]
            ]

        return clade


# ---------------------------------------------------------
# Output


class Writer:
    """Based on the writer in Bio.Nexus.Trees (str, to_string)."""

    def __init__(self, trees):
        """Initialize parameters for NeXML writer."""
        self.trees = trees

        self.node_counter = 0
        self.edge_counter = 0
        self.tree_counter = 0

    def new_label(self, obj_type):
        """Create new labels for the NeXML writer."""
        counter = f"{obj_type}_counter"
        setattr(self, counter, getattr(self, counter) + 1)
        return f"{obj_type}{getattr(self, counter)}"

    def write(self, handle, cdao_to_obo=True, **kwargs):
        """Write this instance's trees to a file handle."""
        self.cdao_to_obo = cdao_to_obo

        # set XML namespaces
        root_node = ElementTree.Element("nex:nexml")
        root_node.set("version", VERSION)
        root_node.set("xmlns", DEFAULT_NAMESPACE)
        root_node.set("xsi:schemaLocation", SCHEMA)

        for prefix, uri in NAMESPACES.items():
            root_node.set(f"xmlns:{prefix}", uri)

        otus = ElementTree.SubElement(
            root_node, "otus", **{"id": "tax", "label": "RootTaxaBlock"}
        )

        # create trees
        trees = ElementTree.SubElement(
            root_node,
            "trees",
            **{"id": "Trees", "label": "TreesBlockFromXML", "otus": "tax"},
        )
        count = 0
        tus = set()
        for tree in self.trees:
            this_tree = ElementTree.SubElement(
                trees, "tree", **{"id": self.new_label("tree")}
            )

            first_clade = tree.clade
            tus.update(self._write_tree(first_clade, this_tree, rooted=tree.rooted))

            count += 1

        # create OTUs
        for tu in tus:
            otu = ElementTree.SubElement(otus, "otu", **{"id": tu})

        # write XML document to file handle
        # xml_doc = ElementTree.ElementTree(root_node)
        # xml_doc.write(handle,
        #              xml_declaration=True, encoding='utf-8',
        #              method='xml')

        # use xml.dom.minodom for pretty printing
        rough_string = ElementTree.tostring(root_node, "utf-8")
        reparsed = minidom.parseString(rough_string)
        try:
            # XML handles ought to be in binary mode
            handle.write(reparsed.toprettyxml(indent="  ").encode("utf8"))
        except TypeError:
            # Fall back for text mode
            handle.write(reparsed.toprettyxml(indent="  "))

        return count

    def _write_tree(self, clade, tree, parent=None, rooted=False):
        """Recursively process tree, adding nodes and edges to Tree object (PRIVATE).

        Returns a set of all OTUs encountered.
        """
        tus = set()

        convert_uri = cdao_to_obo if self.cdao_to_obo else (lambda s: s)

        node_id = self.new_label("node")
        clade.node_id = node_id
        attrib = {"id": node_id, "label": node_id}
        root = rooted and parent is None
        if root:
            attrib["root"] = "true"
        if clade.name:
            tus.add(clade.name)
            attrib["otu"] = clade.name
        node = ElementTree.SubElement(tree, "node", **attrib)

        if parent is not None:
            edge_id = self.new_label("edge")
            attrib = {
                "id": edge_id,
                "source": parent.node_id,
                "target": node_id,
                "length": str(clade.branch_length),
                "typeof": convert_uri("cdao:Edge"),
            }
            try:
                confidence = clade.confidence
            except AttributeError:
                pass
            else:
                if confidence is not None:
                    attrib.update(
                        {
                            "property": convert_uri("cdao:has_Support_Value"),
                            "datatype": "xsd:float",
                            "content": f"{confidence:1.2f}",
                        }
                    )
            node = ElementTree.SubElement(tree, "edge", **attrib)

        if not clade.is_terminal():
            for new_clade in clade.clades:
                tus.update(self._write_tree(new_clade, tree, parent=clade))

        del clade.node_id

        return tus