react-bio-viz 0.1.0__py3-none-any.whl

react_bio_viz/__init__.py

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+"""Jupyter widgets for biological data visualization.
+
+Thin `anywidget <https://anywidget.dev>`_ bindings around the ``react-bio-viz`` React components.
+Every piece of interactive state is a synced traitlet, so the kernel can both drive and observe it::
+
+    from react_bio_viz import MSA
+
+    widget = MSA(msa=[{"header": "seq1", "sequence": "ACGT"}])
+    widget.observe(lambda change: print(change["new"]), names="viewport")
+    widget                      # renders in the notebook
+    widget.viewport = {...}     # drives the view from Python
+
+Each trait is bridged to the component as a ``StoreController``, the same external-store seam a
+JavaScript app fills with a Zustand store — the components themselves contain no Jupyter-specific
+code.
+"""
+
+from ._base import BioVizWidget, fit_to_extent
+from .blasthitdistribution import BlastHitDistribution
+from .distancematrix import DistanceMatrix
+from .genemodel import GeneModel
+from .genomebrowser import GenomeBrowser
+from .io import parse_fasta, parse_newick, read_fasta, read_newick, to_newick
+from .msa import MSA
+from .phylotree import PhyloTree
+
+__version__ = "0.1.0"
+
+__all__ = [
+    "BioVizWidget",
+    "BlastHitDistribution",
+    "DistanceMatrix",
+    "GeneModel",
+    "GenomeBrowser",
+    "MSA",
+    "PhyloTree",
+    "fit_to_extent",
+    "parse_fasta",
+    "parse_newick",
+    "read_fasta",
+    "read_newick",
+    "to_newick",
+    "__version__",
+]

react_bio_viz/_base.py

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+"""Shared plumbing for every react-bio-viz widget."""
+
+from __future__ import annotations
+
+import pathlib
+from typing import Any, Callable, Mapping
+
+import anywidget
+import traitlets
+
+_STATIC = pathlib.Path(__file__).parent / "static"
+
+#: One bundle serves every widget, dispatching on the ``_component`` trait, so React ships once.
+_ESM = _STATIC / "widget.js"
+_CSS = _STATIC / "widget.css"
+
+
+def fit_to_extent(extent: Mapping[str, float]) -> dict[str, float]:
+    """A viewport showing the full extent, i.e. fully zoomed out — ``fitToExtent`` in the JS core."""
+    return {
+        "x0": extent["xMin"],
+        "x1": extent["xMax"],
+        "y0": extent["yMin"],
+        "y1": extent["yMax"],
+        "xMin": extent["xMin"],
+        "xMax": extent["xMax"],
+        "yMin": extent["yMin"],
+        "yMax": extent["yMax"],
+    }
+
+
+class BioVizWidget(anywidget.AnyWidget):
+    """Base class for the react-bio-viz Jupyter widgets.
+
+    Every piece of interactive state is a synced trait, observable and writable from the kernel::
+
+        widget = MSA(msa=records)
+        widget.observe(lambda change: print(change["new"]), names="viewport")
+        widget.viewport = {...}   # drives the view from the kernel
+    """
+
+    _esm = _ESM
+    _css = _CSS
+
+    #: Selects which React component the shared bundle renders.
+    _component = traitlets.Unicode("").tag(sync=True)
+
+    #: The visible window, as a plain ``Viewport`` dict. Seeded on construction so it is readable
+    #: and observable before the user has interacted with the widget.
+    viewport = traitlets.Dict(allow_none=True, default_value=None).tag(sync=True)
+
+    def __init__(self, **kwargs: Any) -> None:
+        super().__init__(**kwargs)
+        if self.viewport is None:
+            extent = self._default_extent()
+            if extent is not None:
+                self.viewport = fit_to_extent(extent)
+
+    def _default_extent(self) -> dict[str, float] | None:
+        """The data extent this widget's viewport spans, or ``None`` if it has no viewport."""
+        return None
+
+    def _on_event(self, event: str, callback: Callable[..., None], *fields: str) -> None:
+        """Calls ``callback`` with ``fields`` of every ``event`` message the component sends.
+
+        One-off user actions (a rename, a click) arrive as custom messages, not traits: a trait would
+        drop the second of two identical events.
+        """
+
+        def handler(_widget: Any, content: Mapping[str, Any], _buffers: Any) -> None:
+            if isinstance(content, Mapping) and content.get("event") == event:
+                callback(*(content.get(field) for field in fields))
+
+        self.on_msg(handler)

react_bio_viz/blasthitdistribution.py

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+"""BLAST hit distribution widget."""
+
+from __future__ import annotations
+
+from typing import Any
+
+import traitlets
+
+from ._base import BioVizWidget
+
+
+class BlastHitDistribution(BioVizWidget):
+    """BLAST hits along one query sequence, row-stacked and colored by a chosen metric.
+
+    :param hits: ``[{"id", "queryId", "subjectId", "queryStart", "queryEnd", "evalue",
+        "bitScore", "percentIdentity"}, ...]``.
+    :param selection: ``{"selectedHitIds": [...]}``; clicking a hit toggles it and writes this back.
+    :param metric: ``"evalue"``, ``"bitScore"`` or ``"percentIdentity"``; written back when the
+        user picks another in the widget's selector.
+
+    >>> w = BlastHitDistribution(hits=hits, query_length=2000)
+    >>> w.observe(lambda c: print(c["new"]["selectedHitIds"]), names="selection")
+    """
+
+    _component = traitlets.Unicode("blasthitdistribution").tag(sync=True)
+
+    hits = traitlets.List(traitlets.Dict(), default_value=[]).tag(sync=True)
+    query_length = traitlets.Int(0).tag(sync=True)
+    query_name = traitlets.Unicode("").tag(sync=True)
+    width = traitlets.Int(800).tag(sync=True)
+    show_scale = traitlets.Bool(True).tag(sync=True)
+    metric = traitlets.Enum(["evalue", "bitScore", "percentIdentity"], default_value="evalue").tag(sync=True)
+
+    selection = traitlets.Dict(allow_none=True, default_value=None).tag(sync=True)
+
+    def __init__(self, **kwargs: Any) -> None:
+        super().__init__(**kwargs)
+        if self.selection is None:
+            self.selection = {"selectedHitIds": []}
+
+    def _default_extent(self) -> dict[str, float] | None:
+        if not self.query_length:
+            return None
+        return {"xMin": 0, "xMax": self.query_length, "yMin": 0, "yMax": 1}

react_bio_viz/distancematrix.py

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+"""Pairwise distance matrix widget."""
+
+from __future__ import annotations
+
+import traitlets
+
+from ._base import BioVizWidget
+
+
+class DistanceMatrix(BioVizWidget):
+    """A pairwise distance matrix as a heatmap, windowed so it scales to thousands of rows.
+
+    :param labels: Row/column ids, in ``matrix`` order.
+    :param matrix: Symmetric ``len(labels)`` × ``len(labels)`` list of lists.
+    :param label_names: Optional ``{id: display name}``.
+    :param options: ``{"showNumbers": bool, "colorScheme": "warm" | "cool" | "green" | "grayscale"}``.
+    :param row_order: Display order of rows (and columns), as ids; written back when labels are
+        dragged. Same shape as :class:`MSA`'s, so the two can be linked.
+
+    >>> w = DistanceMatrix(labels=["a", "b"], matrix=[[0, 0.1], [0.1, 0]])
+    >>> w.observe(print, names="row_order")
+    """
+
+    _component = traitlets.Unicode("distancematrix").tag(sync=True)
+
+    labels = traitlets.List(traitlets.Unicode(), default_value=[]).tag(sync=True)
+    matrix = traitlets.List(traitlets.List(traitlets.Float()), default_value=[]).tag(sync=True)
+    label_names = traitlets.Dict(allow_none=True, default_value=None).tag(sync=True)
+    width = traitlets.Int(650).tag(sync=True)
+    height = traitlets.Int(500).tag(sync=True)
+    options = traitlets.Dict(allow_none=True, default_value=None).tag(sync=True)
+
+    row_order = traitlets.List(traitlets.Unicode(), default_value=[]).tag(sync=True)
+    panel_sizes = traitlets.Dict(default_value={"labelWidth": 160}).tag(sync=True)
+
+    def _default_extent(self) -> dict[str, float] | None:
+        if not self.labels:
+            return None
+        n = len(self.labels)
+        return {"xMin": 0, "xMax": n, "yMin": 0, "yMax": n}

react_bio_viz/genemodel.py

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+"""Gene model widget."""
+
+from __future__ import annotations
+
+import traitlets
+
+from ._base import BioVizWidget
+
+#: Fraction of the gene's length padded onto each side of the default view, mirroring the
+#: component's own ``VIEWPORT_PADDING_RATIO``.
+_PADDING_RATIO = 0.1
+
+
+class GeneModel(BioVizWidget):
+    """A (potentially spliced) gene model: transcripts with their exons and CDSs.
+
+    :param gene: A gff3-shaped ``SequenceInterval`` dict, with nested ``children``.
+
+    >>> w = GeneModel(gene=gff3_record)
+    >>> w.viewport = {**w.viewport, "x0": 35_040_000, "x1": 35_042_000}   # zoom from the kernel
+    """
+
+    _component = traitlets.Unicode("genemodel").tag(sync=True)
+
+    gene = traitlets.Dict(default_value={}).tag(sync=True)
+    width = traitlets.Int(500).tag(sync=True)
+    color_seed = traitlets.Unicode("42").tag(sync=True)
+    show_scale = traitlets.Bool(True).tag(sync=True)
+
+    def _default_extent(self) -> dict[str, float] | None:
+        start, end = self.gene.get("start"), self.gene.get("end")
+        if start is None or end is None:
+            return None
+        padding = round(_PADDING_RATIO * (end - start))
+        return {"xMin": max(0, start - padding), "xMax": end + padding, "yMin": 0, "yMax": 1}

react_bio_viz/genomebrowser.py

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+"""Multi-track genome browser widget."""
+
+from __future__ import annotations
+
+import traitlets
+
+from ._base import BioVizWidget
+
+
+class GenomeBrowser(BioVizWidget):
+    """Stacked genome tracks sharing one genomic-coordinate viewport.
+
+    :param tracks: ``[{"id", "label", "kind", "data"}, ...]`` where ``kind`` is one of
+        ``"feature"``, ``"coverage"`` or ``"genemodel"``.
+    :param reference_length: Length of the reference sequence; the x-axis extent.
+
+    >>> w = GenomeBrowser(tracks=tracks, reference_length=35_045_433)
+    """
+
+    _component = traitlets.Unicode("genomebrowser").tag(sync=True)
+
+    tracks = traitlets.List(traitlets.Dict(), default_value=[]).tag(sync=True)
+    reference_length = traitlets.Int(0).tag(sync=True)
+    reference_name = traitlets.Unicode("").tag(sync=True)
+    width = traitlets.Int(1000).tag(sync=True)
+    show_scale = traitlets.Bool(True).tag(sync=True)
+
+    def _default_extent(self) -> dict[str, float] | None:
+        if not self.reference_length:
+            return None
+        return {"xMin": 0, "xMax": self.reference_length, "yMin": 0, "yMax": 1}

react_bio_viz/io.py

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+"""Reading alignments and trees into the plain structures the widgets take.
+
+The widgets take plain JSON-able data — a list of ``{"header", "sequence"}`` records for
+:class:`~react_bio_viz.MSA`, nested ``{"name", "length", "children"}`` dicts for
+:class:`~react_bio_viz.PhyloTree` — so any parser works. These cover the common formats without
+extra dependencies, and parse Newick the same way the JavaScript ``parseNewick`` does.
+"""
+
+from __future__ import annotations
+
+import os
+import re
+from typing import Any, Union
+
+PathLike = Union[str, "os.PathLike[str]"]
+
+Record = dict[str, str]
+TreeNode = dict[str, Any]
+
+
+def parse_fasta(text: str) -> list[Record]:
+    """Parses FASTA text into ``[{"header": ..., "sequence": ...}, ...]``.
+
+    The header is the whole line after ``>``; sequence lines are joined with whitespace removed.
+    """
+    records: list[Record] = []
+    for line in text.splitlines():
+        line = line.strip()
+        if not line:
+            continue
+        if line.startswith(">"):
+            records.append({"header": line[1:].strip(), "sequence": ""})
+        elif records:
+            records[-1]["sequence"] += re.sub(r"\s+", "", line)
+        else:
+            raise ValueError("FASTA text must start with a '>' header line")
+    return records
+
+
+def read_fasta(path: PathLike) -> list[Record]:
+    """Reads a FASTA file — see :func:`parse_fasta`."""
+    with open(path, encoding="utf-8") as handle:
+        return parse_fasta(handle.read())
+
+
+def parse_newick(text: str) -> TreeNode:
+    """Parses a Newick string into nested ``{"name", "length", "children"}`` dicts.
+
+    Internal-node labels (typically bootstrap support) become the node's ``name``; ``:length``
+    suffixes become ``length`` (0 when absent). Quoted labels (``'a b'``, with ``''`` for a literal
+    quote) are unquoted, so FASTA-style names with spaces or ``|`` survive a round trip.
+    """
+    position = 0
+
+    def skip_space() -> None:
+        nonlocal position
+        while position < len(text) and text[position].isspace():
+            position += 1
+
+    def parse_label() -> str:
+        nonlocal position
+        skip_space()
+        if position < len(text) and text[position] in "'\"":
+            quote = text[position]
+            position += 1
+            label = []
+            while position < len(text):
+                if text[position] == quote:
+                    if position + 1 < len(text) and text[position + 1] == quote:
+                        label.append(quote)
+                        position += 2
+                        continue
+                    position += 1
+                    break
+                label.append(text[position])
+                position += 1
+            return "".join(label)
+        start = position
+        while position < len(text) and text[position] not in ":,();":
+            position += 1
+        return text[start:position].strip()
+
+    def parse_node() -> TreeNode:
+        nonlocal position
+        node: TreeNode = {"name": "", "length": 0.0, "children": []}
+        skip_space()
+        if position < len(text) and text[position] == "(":
+            position += 1
+            node["children"].append(parse_node())
+            skip_space()
+            while position < len(text) and text[position] == ",":
+                position += 1
+                node["children"].append(parse_node())
+                skip_space()
+            if position < len(text) and text[position] == ")":
+                position += 1
+        node["name"] = parse_label()
+        skip_space()
+        if position < len(text) and text[position] == ":":
+            position += 1
+            start = position
+            while position < len(text) and text[position] not in ",);":
+                position += 1
+            try:
+                node["length"] = float(text[start:position])
+            except ValueError:
+                node["length"] = 0.0
+        return node
+
+    return parse_node()
+
+
+def read_newick(path: PathLike) -> TreeNode:
+    """Reads a Newick file — see :func:`parse_newick`."""
+    with open(path, encoding="utf-8") as handle:
+        return parse_newick(handle.read())
+
+
+def _quote(name: str) -> str:
+    return f"'{name.replace(chr(39), chr(39) * 2)}'" if re.search(r"[\s:,;()\[\]']", name) else name
+
+
+def to_newick(tree: TreeNode) -> str:
+    """Serializes nested ``{"name", "length", "children"}`` dicts to Newick, quoting names as needed."""
+
+    def write(node: TreeNode, is_root: bool) -> str:
+        children = node.get("children") or []
+        inner = "(" + ",".join(write(child, False) for child in children) + ")" if children else ""
+        length = node.get("length") or 0
+        suffix = "" if is_root and not length else f":{length:g}"
+        return f"{inner}{_quote(node.get('name', ''))}{suffix}"
+
+    return write(tree, True) + ";"

react_bio_viz/msa.py

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+"""Multiple sequence alignment widget."""
+
+from __future__ import annotations
+
+from typing import Any, Callable
+
+import traitlets
+
+from ._base import BioVizWidget
+
+
+class MSA(BioVizWidget):
+    """A multiple sequence alignment, with pan/zoom, a column ruler, a minimap and a consensus row.
+
+    :param msa: The alignment, as ``[{"header": ..., "sequence": ...}, ...]``.
+    :param options: Rendering toggles, mirroring ``MSADrawOptions`` (camelCase keys, e.g.
+        ``{"colorStyle": "AA Zappo", "tracks": ["conservation", "logo"]}``). Omitting
+        ``colorStyle`` lets the component pick a scheme from the alignment's own alphabet.
+    :param selection: Selected rows (by id — a record's ``id``, else its ``header``) and columns,
+        ``{"rows": [...], "columns": [...]}``; written back as the user selects.
+    :param row_order: Display order of the rows, as ids; written back when labels are dragged.
+    :param panel_sizes: ``{"labelWidth", "trackHeight", "minimapHeight"}`` in pixels.
+
+    The widget never edits ``msa`` itself: register :meth:`on_rename_row`,
+    :meth:`on_remove_rows` or :meth:`on_remove_columns` to apply edits (which also enables them).
+
+    >>> w = MSA(msa=[{"header": "a", "sequence": "ACGT"}])
+    >>> w.observe(print, names="viewport")   # fires when the user pans or zooms
+    >>> w.observe(print, names="selection")
+    """
+
+    _component = traitlets.Unicode("msa").tag(sync=True)
+
+    msa = traitlets.List(traitlets.Dict(), default_value=[]).tag(sync=True)
+    width = traitlets.Int(650).tag(sync=True)
+    height = traitlets.Int(400).tag(sync=True)
+    options = traitlets.Dict(allow_none=True, default_value=None).tag(sync=True)
+
+    selection = traitlets.Dict(default_value={"rows": [], "columns": []}).tag(sync=True)
+    row_order = traitlets.List(traitlets.Unicode(), default_value=[]).tag(sync=True)
+    panel_sizes = traitlets.Dict(
+        default_value={"labelWidth": 150, "trackHeight": 48, "minimapHeight": 50}
+    ).tag(sync=True)
+
+    def on_rename_row(self, callback: Callable[[str, str], Any]) -> None:
+        """Calls ``callback(row_id, new_name)`` when the user renames a row label."""
+        self._on_event("rename_row", callback, "row_id", "name")
+
+    def on_remove_rows(self, callback: Callable[[list[str]], Any]) -> None:
+        """Calls ``callback(row_ids)`` when the user removes rows (× on a label, or Delete)."""
+        self._on_event("remove_rows", callback, "row_ids")
+
+    def on_remove_columns(self, callback: Callable[[list[int]], Any]) -> None:
+        """Calls ``callback(columns)`` when the user deletes selected columns."""
+        self._on_event("remove_columns", callback, "columns")
+
+    def _default_extent(self) -> dict[str, float] | None:
+        if not self.msa:
+            return None
+        columns = len(self.msa[0].get("sequence", ""))
+        return {"xMin": 0, "xMax": columns, "yMin": 0, "yMax": len(self.msa)}

react_bio_viz/phylotree.py

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+"""Phylogenetic tree widget."""
+
+from __future__ import annotations
+
+from typing import Any, Callable
+
+import traitlets
+
+from ._base import BioVizWidget
+
+
+class PhyloTree(BioVizWidget):
+    """A phylogenetic tree in rectangular, cladogram or radial layout.
+
+    :param tree: Recursively nested ``{"name": ..., "length": ..., "children": [...]}``.
+    :param selection: Where the tree is rooted and how it is arranged —
+        ``{"rerootedAt": str | None, "rerootPosition": float, "collapsed": [str], "order": {...}}``.
+        Writable from the kernel and written back when the user collapses, drags or reroots.
+    :param node_styles: ``{node_id: {"color": ..., "bold": ...}}``.
+    :param branch_styles: ``{node_id: {"color": ...}}`` for the branch above each node.
+    :param leaf_order: Read-only: leaf names in display order, updated as the user rearranges.
+
+    >>> w = PhyloTree(tree=newick_dict, tree_layout="radial", interactive=True)
+    >>> w.observe(lambda c: print(c["new"]["collapsed"]), names="selection")
+    >>> w.on_node_click(lambda node: print(node["id"], node["leafNames"]))
+    """
+
+    _component = traitlets.Unicode("phylotree").tag(sync=True)
+
+    tree = traitlets.Dict(default_value={}).tag(sync=True)
+    width = traitlets.Int(1000).tag(sync=True)
+    height = traitlets.Int(900).tag(sync=True)
+    #: ``"rectangular"``, ``"cladogram"`` or ``"radial"``. Not called ``layout``: every ipywidgets
+    #: widget already has a ``layout`` trait (its CSS layout), and shadowing it breaks the view.
+    tree_layout = traitlets.Enum(
+        ["rectangular", "cladogram", "radial"], default_value="rectangular"
+    ).tag(sync=True)
+    show_support_values = traitlets.Bool(True).tag(sync=True)
+    shade_branch_by_support = traitlets.Bool(True).tag(sync=True)
+    font_size = traitlets.Int(10).tag(sync=True)
+    align_tips = traitlets.Bool(True).tag(sync=True)
+    interactive = traitlets.Bool(False).tag(sync=True)
+    search_query = traitlets.Unicode(allow_none=True, default_value=None).tag(sync=True)
+    search_use_regex = traitlets.Bool(False).tag(sync=True)
+    show_scale_bar = traitlets.Bool(True).tag(sync=True)
+    show_branch_lengths = traitlets.Bool(False).tag(sync=True)
+    support_threshold = traitlets.Float(0).tag(sync=True)
+    drag_enabled = traitlets.Bool(allow_none=True, default_value=None).tag(sync=True)
+    branch_width = traitlets.Float(0.75).tag(sync=True)
+    node_radius = traitlets.Float(4).tag(sync=True)
+    label_font_size = traitlets.Float(11).tag(sync=True)
+    leaf_spacing = traitlets.Float(allow_none=True, default_value=None).tag(sync=True)
+    leaf_marker_color = traitlets.Unicode(allow_none=True, default_value=None).tag(sync=True)
+    node_styles = traitlets.Dict(default_value={}).tag(sync=True)
+    branch_styles = traitlets.Dict(default_value={}).tag(sync=True)
+    active_node_id = traitlets.Unicode(allow_none=True, default_value=None).tag(sync=True)
+    leaf_order = traitlets.List(traitlets.Unicode(), default_value=[]).tag(sync=True)
+
+    selection = traitlets.Dict(allow_none=True, default_value=None).tag(sync=True)
+
+    def __init__(self, **kwargs: Any) -> None:
+        # Accept the React prop's name as a convenience; a string can only mean the tree layout
+        # (ipywidgets' own `layout` takes a Layout widget or a dict).
+        if isinstance(kwargs.get("layout"), str):
+            kwargs["tree_layout"] = kwargs.pop("layout")
+        super().__init__(**kwargs)
+        if self.selection is None:
+            self.selection = {"collapsed": []}
+
+    def on_node_click(self, callback: Callable[[dict[str, Any]], Any]) -> None:
+        """Calls ``callback(node)`` when a node marker is clicked (see ``TreeNodeInfo``)."""
+        self._on_event("node_click", callback, "node")
+
+    def on_branch_click(self, callback: Callable[[dict[str, Any]], Any]) -> None:
+        """Calls ``callback(node)`` — the node below the branch — when a branch is clicked."""
+        self._on_event("branch_click", callback, "node")
+
+    def _default_extent(self) -> dict[str, float] | None:
+        # The tree's pan/zoom is over the rendered pixel surface, not over data coordinates.
+        return {"xMin": 0, "xMax": self.width, "yMin": 0, "yMax": self.height}

react_bio_viz/static/widget.css

@@ -0,0 +1,2 @@
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+/*! tailwindcss v4.3.3 | MIT License | https://tailwindcss.com */