dash-seqviz 0.1.0__py3-none-any.whl

dash_seqviz/SeqViz.py

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+# AUTO GENERATED FILE - DO NOT EDIT
+
+import typing  # noqa: F401
+from typing_extensions import TypedDict, NotRequired, Literal # noqa: F401
+from dash.development.base_component import Component, _explicitize_args
+
+ComponentType = typing.Union[
+    str,
+    int,
+    float,
+    Component,
+    None,
+    typing.Sequence[typing.Union[str, int, float, Component, None]],
+]
+
+NumberType = typing.Union[
+    typing.SupportsFloat, typing.SupportsInt, typing.SupportsComplex
+]
+
+
+class SeqViz(Component):
+    """A SeqViz component.
+SeqViz is a Dash wrapper for the seqviz JavaScript library.
+It provides DNA, RNA, and protein sequence visualization with
+circular and linear viewers, annotations, primers, and more.
+
+Keyword arguments:
+
+- id (string; optional):
+    The ID used to identify this component in Dash callbacks.
+
+- accession (string; optional):
+    (Deprecated upstream) NCBI accession ID. Prefer parsing with
+    seqparse.
+
+- annotations (list of dicts; optional):
+    Array of annotation objects to render. Each annotation: { start:
+    number, end: number, name: string, direction?: number, color?:
+    string }.
+
+    `annotations` is a list of dicts with keys:
+
+    - start (number; required)
+
+    - end (number; required)
+
+    - name (string; required)
+
+    - direction (number; optional)
+
+    - color (string; optional)
+
+- bpColors (dict; optional):
+    Object mapping base pairs or indexes to custom colors.
+
+- colors (list of strings; optional):
+    Array of colors for annotations, translations, and highlights.
+
+- disableExternalFonts (boolean; default False):
+    Whether to disable downloading external fonts.
+
+- enableCopyEvent (boolean; default True):
+    When False, disables the default copyEvent (ctrl/cmd + C).
+
+- enableSelectAllEvent (boolean; default True):
+    When False, disables the default selectAllEvent (ctrl/cmd + A).
+
+- enzymes (list of dicts; optional):
+    Array of restriction enzymes. Can be enzyme names (strings) or
+    custom enzyme objects.
+
+    `enzymes` is a list of string | dict with keys:
+
+    - name (string; required)
+
+    - rseq (string; required)
+
+    - fcut (number; required)
+
+    - rcut (number; required)
+
+    - color (string; optional)
+
+    - range (dict; optional)
+
+        `range` is a dict with keys:
+
+        - start (number; optional)
+
+        - end (number; optional)s
+
+- file (string | dict; optional):
+    (Deprecated upstream) Sequence file or URL. Prefer parsing with
+    seqparse.
+
+- highlights (list of dicts; optional):
+    Array of highlight objects. Each highlight: { start: number, end:
+    number, color?: string }.
+
+    `highlights` is a list of dicts with keys:
+
+    - start (number; required)
+
+    - end (number; required)
+
+    - color (string; optional)
+
+- name (string; optional):
+    The name of the sequence/plasmid. Shown at the center of the
+    circular viewer.
+
+- primers (list of dicts; optional):
+    Array of primer objects to render. Each primer: { start: number,
+    end: number, name: string, direction: number, color?: string }.
+
+    `primers` is a list of dicts with keys:
+
+    - start (number; required)
+
+    - end (number; required)
+
+    - name (string; required)
+
+    - direction (number; required)
+
+    - color (string; optional)
+
+- rotateOnScroll (boolean; default True):
+    Whether the circular viewer rotates on scroll.
+
+- search (dict; optional):
+    Search configuration object. { query: string, mismatch?: number }.
+
+    `search` is a dict with keys:
+
+    - query (string; required)
+
+    - mismatch (number; optional)
+
+- searchResults (list; optional):
+    Search results emitted by seqviz (read-only for Dash usage).
+
+- selection (dict; optional):
+    Selection state object. { start: number, end: number, clockwise?:
+    boolean }.
+
+    `selection` is a dict with keys:
+
+    - start (number; required)
+
+    - end (number; required)
+
+    - clockwise (boolean; optional)
+
+- seq (string; optional):
+    The sequence to render. Can be DNA, RNA, or amino acid sequence.
+
+- showComplement (boolean; default True):
+    Whether to show the complement sequence.
+
+- translations (list of dicts; optional):
+    Array of translation objects. Each translation: { start: number,
+    end: number, direction: number, name?: string, color?: string }.
+
+    `translations` is a list of dicts with keys:
+
+    - start (number; required)
+
+    - end (number; required)
+
+    - direction (number; required)
+
+    - name (string; optional)
+
+    - color (string; optional)
+
+- viewer (a value equal to: 'linear', 'circular', 'both', 'both_flip'; default 'both'):
+    The type and orientation of the sequence viewers. Options:
+    \"linear\", \"circular\", \"both\", \"both_flip\".
+
+- zoom (dict; default { linear: 50 }):
+    Zoom configuration object. Currently supports: { linear: number }
+    (0-100).
+
+    `zoom` is a dict with keys:
+
+    - linear (number; optional)"""
+    _children_props = []
+    _base_nodes = ['children']
+    _namespace = 'dash_seqviz'
+    _type = 'SeqViz'
+    Annotations = TypedDict(
+        "Annotations",
+            {
+            "start": NumberType,
+            "end": NumberType,
+            "name": str,
+            "direction": NotRequired[NumberType],
+            "color": NotRequired[str]
+        }
+    )
+
+    Primers = TypedDict(
+        "Primers",
+            {
+            "start": NumberType,
+            "end": NumberType,
+            "name": str,
+            "direction": NumberType,
+            "color": NotRequired[str]
+        }
+    )
+
+    Highlights = TypedDict(
+        "Highlights",
+            {
+            "start": NumberType,
+            "end": NumberType,
+            "color": NotRequired[str]
+        }
+    )
+
+    Translations = TypedDict(
+        "Translations",
+            {
+            "start": NumberType,
+            "end": NumberType,
+            "direction": NumberType,
+            "name": NotRequired[str],
+            "color": NotRequired[str]
+        }
+    )
+
+    EnzymesRange = TypedDict(
+        "EnzymesRange",
+            {
+            "start": NotRequired[NumberType],
+            "end": NotRequired[NumberType]
+        }
+    )
+
+    Enzymes = TypedDict(
+        "Enzymes",
+            {
+            "name": str,
+            "rseq": str,
+            "fcut": NumberType,
+            "rcut": NumberType,
+            "color": NotRequired[str],
+            "range": NotRequired["EnzymesRange"]
+        }
+    )
+
+    Search = TypedDict(
+        "Search",
+            {
+            "query": str,
+            "mismatch": NotRequired[NumberType]
+        }
+    )
+
+    Selection = TypedDict(
+        "Selection",
+            {
+            "start": NumberType,
+            "end": NumberType,
+            "clockwise": NotRequired[bool]
+        }
+    )
+
+    Zoom = TypedDict(
+        "Zoom",
+            {
+            "linear": NotRequired[NumberType]
+        }
+    )
+
+
+    def __init__(
+        self,
+        id: typing.Optional[typing.Union[str, dict]] = None,
+        seq: typing.Optional[str] = None,
+        file: typing.Optional[typing.Union[str, dict]] = None,
+        accession: typing.Optional[str] = None,
+        name: typing.Optional[str] = None,
+        viewer: typing.Optional[Literal["linear", "circular", "both", "both_flip"]] = None,
+        annotations: typing.Optional[typing.Sequence["Annotations"]] = None,
+        primers: typing.Optional[typing.Sequence["Primers"]] = None,
+        highlights: typing.Optional[typing.Sequence["Highlights"]] = None,
+        translations: typing.Optional[typing.Sequence["Translations"]] = None,
+        enzymes: typing.Optional[typing.Sequence[typing.Union[str, "Enzymes"]]] = None,
+        search: typing.Optional["Search"] = None,
+        selection: typing.Optional["Selection"] = None,
+        colors: typing.Optional[typing.Sequence[str]] = None,
+        bpColors: typing.Optional[dict] = None,
+        style: typing.Optional[typing.Any] = None,
+        zoom: typing.Optional["Zoom"] = None,
+        showComplement: typing.Optional[bool] = None,
+        rotateOnScroll: typing.Optional[bool] = None,
+        disableExternalFonts: typing.Optional[bool] = None,
+        onSelection: typing.Optional[typing.Any] = None,
+        onSearch: typing.Optional[typing.Any] = None,
+        enableCopyEvent: typing.Optional[bool] = None,
+        enableSelectAllEvent: typing.Optional[bool] = None,
+        searchResults: typing.Optional[typing.Sequence] = None,
+        **kwargs
+    ):
+        self._prop_names = ['id', 'accession', 'annotations', 'bpColors', 'colors', 'disableExternalFonts', 'enableCopyEvent', 'enableSelectAllEvent', 'enzymes', 'file', 'highlights', 'name', 'primers', 'rotateOnScroll', 'search', 'searchResults', 'selection', 'seq', 'showComplement', 'style', 'translations', 'viewer', 'zoom']
+        self._valid_wildcard_attributes =            []
+        self.available_properties = ['id', 'accession', 'annotations', 'bpColors', 'colors', 'disableExternalFonts', 'enableCopyEvent', 'enableSelectAllEvent', 'enzymes', 'file', 'highlights', 'name', 'primers', 'rotateOnScroll', 'search', 'searchResults', 'selection', 'seq', 'showComplement', 'style', 'translations', 'viewer', 'zoom']
+        self.available_wildcard_properties =            []
+        _explicit_args = kwargs.pop('_explicit_args')
+        _locals = locals()
+        _locals.update(kwargs)  # For wildcard attrs and excess named props
+        args = {k: _locals[k] for k in _explicit_args}
+
+        super(SeqViz, self).__init__(**args)
+
+setattr(SeqViz, "__init__", _explicitize_args(SeqViz.__init__))

dash_seqviz/__init__.py

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+from __future__ import print_function as _
+
+import os as _os
+import sys as _sys
+import json
+
+import dash as _dash
+
+# noinspection PyUnresolvedReferences
+from ._imports_ import *
+from ._imports_ import __all__
+
+if not hasattr(_dash, '__plotly_dash') and not hasattr(_dash, 'development'):
+    print('Dash was not successfully imported. '
+          'Make sure you don\'t have a file '
+          'named \n"dash.py" in your current directory.', file=_sys.stderr)
+    _sys.exit(1)
+
+_basepath = _os.path.dirname(__file__)
+_filepath = _os.path.abspath(_os.path.join(_basepath, 'package-info.json'))
+with open(_filepath) as f:
+    package = json.load(f)
+
+package_name = package['name'].replace(' ', '_').replace('-', '_')
+__version__ = package['version']
+
+_current_path = _os.path.dirname(_os.path.abspath(__file__))
+
+_this_module = _sys.modules[__name__]
+
+async_resources = ["SeqViz",]
+
+_js_dist = []
+
+_js_dist.extend(
+    [
+        {
+            "relative_package_path": "async-{}.js".format(async_resource),
+            "external_url": (
+                "https://unpkg.com/{0}@{2}"
+                "/{1}/async-{3}.js"
+            ).format(package_name, __name__, __version__, async_resource),
+            "namespace": package_name,
+            "async": True,
+        }
+        for async_resource in async_resources
+    ]
+)
+
+# TODO: Figure out if unpkg link works
+_js_dist.extend(
+    [
+        {
+            "relative_package_path": "async-{}.js.map".format(async_resource),
+            "external_url": (
+                "https://unpkg.com/{0}@{2}"
+                "/{1}/async-{3}.js.map"
+            ).format(package_name, __name__, __version__, async_resource),
+            "namespace": package_name,
+            "dynamic": True,
+        }
+        for async_resource in async_resources
+    ]
+)
+
+_js_dist.extend(
+    [
+        {
+            'relative_package_path': 'dash_seqviz.min.js',
+    
+            'namespace': package_name
+        },
+        {
+            'relative_package_path': 'dash_seqviz.min.js.map',
+    
+            'namespace': package_name,
+            'dynamic': True
+        }
+    ]
+)
+
+_css_dist = []
+
+
+for _component in __all__:
+    setattr(locals()[_component], '_js_dist', _js_dist)
+    setattr(locals()[_component], '_css_dist', _css_dist)

dash_seqviz/_imports_.py

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+from .SeqViz import SeqViz
+
+__all__ = [
+    "SeqViz"
+]