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| import gradio as gr | |
| from app import demo as app | |
| import os | |
| _docs = {'IGV': {'description': 'IGV Browser component.', 'members': {'__init__': {'value': {'type': 'Any', 'default': 'None', 'description': None}, 'label': {'type': 'str | None', 'default': 'None', 'description': None}, 'info': {'type': 'str | None', 'default': 'None', 'description': None}, 'show_label': {'type': 'bool | None', 'default': 'None', 'description': None}, 'container': {'type': 'bool', 'default': 'True', 'description': None}, 'scale': {'type': 'int | None', 'default': 'None', 'description': None}, 'min_width': {'type': 'int | None', 'default': 'None', 'description': None}, 'interactive': {'type': 'bool | None', 'default': 'None', 'description': None}, 'visible': {'type': 'bool', 'default': 'True', 'description': None}, 'elem_id': {'type': 'str | None', 'default': 'None', 'description': None}, 'elem_classes': {'type': 'list[str] | str | None', 'default': 'None', 'description': None}, 'render': {'type': 'bool', 'default': 'True', 'description': None}, 'key': {'type': 'int | str | None', 'default': 'None', 'description': None}, 'load_fn': {'type': 'Callable | None', 'default': 'None', 'description': None}, 'every': {'type': 'Timer | float | None', 'default': 'None', 'description': None}, 'inputs': {'type': 'Component | Sequence[Component] | set[Component] | None', 'default': 'None', 'description': None}}, 'postprocess': {'value': {'type': 'IGVContext', 'description': None}}, 'preprocess': {'return': {'type': 'IGVContext', 'description': None}, 'value': None}}, 'events': {'trackremoved': {'type': None, 'default': None, 'description': 'Triggered when a track is removed from the IGV Browser.'}, 'trackdrag': {'type': None, 'default': None, 'description': 'Triggered when a track is dragged in the IGV Browser.'}, 'trackdragend': {'type': None, 'default': None, 'description': 'Triggered when a track is finished being dragged in the IGV Browser.'}, 'locuschange': {'type': None, 'default': None, 'description': 'Triggered when the locus is changed in the IGV Browser.'}, 'trackclick': {'type': None, 'default': None, 'description': 'Triggered when a track is clicked in the IGV Browser.'}, 'trackorderchanged': {'type': None, 'default': None, 'description': 'Triggered when the order of tracks is changed in the IGV Browser.'}}}, '__meta__': {'additional_interfaces': {'IGVContext': {'source': 'class IGVContext(GradioModel):\n genome: str | ReferenceGenome = Field(default="hg38")\n locus: str = Field(default="")\n loadAlignmentTracks: list[AlignmentTrackLoad] = Field(\n default_factory=list\n )\n loadVariantTracks: list[VariantTrackLoad] = Field(\n default_factory=list\n )\n loadAnnotationTracks: list[AnnotationTrackLoad] = Field(\n default_factory=list\n )\n removeTracks: list[str] = Field(default_factory=list)\n\n def update_genome(self, genome: str | ReferenceGenome):\n self.genome = genome\n return self\n\n def update_locus(self, locus: str):\n self.locus = locus\n return self\n\n def add_track(self, track_load: TrackLoad):\n if isinstance(track_load, AlignmentTrackLoad):\n self.loadAlignmentTracks.append(track_load)\n elif isinstance(track_load, VariantTrackLoad):\n self.loadVariantTracks.append(track_load)\n elif isinstance(track_load, AnnotationTrackLoad):\n self.loadAnnotationTracks.append(track_load)\n else:\n raise ValueError(\n "TrackLoad type not recognized."\n )\n\n return self\n\n def remove_track(self, track: str):\n self.removeTracks.append(track)\n return self', 'refs': ['ReferenceGenome', 'AlignmentTrackLoad', 'VariantTrackLoad', 'AnnotationTrackLoad']}, 'ReferenceGenome': {'source': 'class ReferenceGenome(GradioModel):\n id: Optional[str] = Field(default="hg38")\n name: Optional[str] = Field(default="hg38")\n fastaURL: Optional[str] = Field(default=None)\n indexURL: Optional[str] = Field(default=None)\n compressedIndexURL: Optional[str] = Field(default=None)\n twoBitURL: Optional[str] = Field(default=None)\n cytobandURL: Optional[str] = Field(default=None)\n aliasURL: Optional[str] = Field(default=None)\n chromSizesURL: Optional[str] = Field(default=None)\n chromosomeOrder: Optional[list[str]] = Field(\n default=None\n )\n headers: Optional[Dict[str, str]] = Field(default=None)\n wholeGenomeView: bool = Field(default=True)'}, 'AlignmentTrackLoad': {'source': 'class AlignmentTrackLoad(TrackLoad):\n showCoverage: bool = True\n showAlignments: bool = True\n viewAsPairs: bool = False\n pairsSupported: bool = True\n coverageColor: Optional[str] = None\n color: str = "rgb(170, 170, 170)"\n deletionColor: str = "black"\n displayMode: str = Field(\n default="EXPANDED",\n pattern="^(FULL|EXPANDED|SQUISHED)$",\n )\n groupBy: Optional[str] = None\n samplingWindowSize: int = 100\n samplingDepth: int = 100\n readGroup: Optional[str] = None\n sort: Optional[AlignmentSortOptions] = None\n filter: Dict[str, bool | int | list[str]] = None\n showSoftClips: bool = False\n showMismatches: bool = True\n showAllBases: bool = False\n showInsertionText: bool = False\n insertionTextColor: str = "white"\n alignmentRowHeight: int = 14\n squishedRowHeight: int = 3\n colorBy: str = "unexpectedPair"\n insertionColor: str = "rgb(138, 94, 161)"\n negStrandColor: str = "rgba(150, 150, 230, 0.75)"', 'refs': ['AlignmentSortOptions']}, 'AlignmentSortOptions': {'source': 'class AlignmentSortOptions(GradioModel):\n chr: str\n position: int\n direction: Optional[str] = Field(\n default="ASC", pattern="^(ASC|DESC)$"\n )\n option: str\n tag: Optional[str] = None'}, 'VariantTrackLoad': {'source': 'class VariantTrackLoad(TrackLoad):\n displayMode: Optional[str] = Field(\n default="EXPANDED",\n pattern="^(EXPANDED|SQUISHED|COLLAPSED)$",\n )\n squishedCallHeight: Optional[int] = 1\n expandedCallHeight: Optional[int] = 10\n color: Optional[str] = None\n colorBy: Optional[str] = None\n colorTable: Optional[Dict[str, str]] = None\n noCallColor: Optional[str] = "rgb(250, 250, 250)"\n homvarColor: Optional[str] = "rgb(17,248,254)"\n hetvarColor: Optional[str] = "rgb(34,12,253)"\n homrefColor: Optional[str] = "rgb(200, 200, 200)"\n supportsWholeGenome: Optional[bool] = None\n showGenotypes: Optional[bool] = None\n # strokecolor: Optional[Callable[[VCFItem], str]] = None\n # context_hook: Optional[Callable[[VCFItem, Draw.CanvasContext, int, int, int, int], None]] = None'}, 'AnnotationTrackLoad': {'source': 'class AnnotationTrackLoad(TrackLoad):\n displayMode: str = Field(\n default="COLLAPSED",\n pattern="^(EXPANDED|SQUISHED|COLLAPSED)$",\n )\n squishedRowHeight: int = 15\n expandedRowHeight: int = 30\n color: str = "rgb(0,0,150)"\n colorBy: Optional[str] = None\n altColor: Optional[str] = None\n colorTable: Optional[Dict[str, str]] = None\n searchable: bool = False\n searchableFields: list[str] = Field(\n default_factory=list\n )\n nameField: Optional[str] = None\n maxRows: int = 500\n filterTypes: Optional[list[str]] = None'}}, 'user_fn_refs': {'IGV': ['IGVContext']}}} | |
| abs_path = os.path.join(os.path.dirname(__file__), "css.css") | |
| with gr.Blocks( | |
| css=abs_path, | |
| theme=gr.themes.Default( | |
| font_mono=[ | |
| gr.themes.GoogleFont("Inconsolata"), | |
| "monospace", | |
| ], | |
| ), | |
| ) as demo: | |
| gr.Markdown( | |
| """ | |
| # `gradio_igv` | |
| <div style="display: flex; gap: 7px;"> | |
| <img alt="Static Badge" src="https://img.shields.io/badge/version%20-%200.1.0%20-%20orange"> | |
| </div> | |
| Embed IGV.js in your app to visualize genomics data. | |
| """, elem_classes=["md-custom"], header_links=True) | |
| app.render() | |
| gr.Markdown( | |
| """ | |
| ## Installation | |
| ```bash | |
| pip install gradio_igv | |
| ``` | |
| ## Usage | |
| ```python | |
| import gradio as gr | |
| from gradio_igv import IGV, IGVContext, AlignmentTrackLoad, FeatureContext, parse_locus | |
| import pandas as pd | |
| public_cram = "https://s3.amazonaws.com/1000genomes/data/HG00103/alignment/HG00103.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram" | |
| default_igv_context = IGVContext( | |
| genome="hg38", | |
| ).update_locus("BRCA1").add_track( | |
| AlignmentTrackLoad( | |
| name="HG00103", | |
| url=public_cram, | |
| indexURL=f"{public_cram}.crai", | |
| order=1, | |
| height=200, | |
| colorBy="strand", | |
| oauthToken=None, # Public file so no auth needed; otherwise inferred by URL type using environment | |
| ) | |
| ) | |
| def summarize_visible_alignments(igv_context): | |
| loci = parse_locus(igv_context.locus) | |
| feature_ctx = FeatureContext( | |
| files=[public_cram], | |
| names=["HG00103"], | |
| loci=loci, | |
| ) | |
| reads = list(feature_ctx.features["HG00103"]) | |
| df = pd.DataFrame({ | |
| "Read Name": [read.query_name for read in reads], | |
| "Pos": [read.reference_start for read in reads], | |
| "MAPQ": [read.mapq for read in reads], | |
| }).sort_values(by='Pos') | |
| return df.head(20) | |
| with gr.Blocks() as demo: | |
| with gr.Row(): | |
| with gr.Column(scale=3): | |
| igv_component = IGV(value=default_igv_context, label="IGV Browser") | |
| with gr.Column(scale=1): | |
| alignment_summary = gr.DataFrame(value=pd.DataFrame(), label="Alignment Summary", max_height=800) | |
| igv_component.locuschange(summarize_visible_alignments, [igv_component], [alignment_summary]) | |
| if __name__ == "__main__": | |
| demo.launch() | |
| ``` | |
| """, elem_classes=["md-custom"], header_links=True) | |
| gr.Markdown(""" | |
| ## `IGV` | |
| ### Initialization | |
| """, elem_classes=["md-custom"], header_links=True) | |
| gr.ParamViewer(value=_docs["IGV"]["members"]["__init__"], linkify=['IGVContext', 'ReferenceGenome', 'AlignmentTrackLoad', 'AlignmentSortOptions', 'VariantTrackLoad', 'AnnotationTrackLoad']) | |
| gr.Markdown("### Events") | |
| gr.ParamViewer(value=_docs["IGV"]["events"], linkify=['Event']) | |
| gr.Markdown(""" | |
| ### User function | |
| The impact on the users predict function varies depending on whether the component is used as an input or output for an event (or both). | |
| - When used as an Input, the component only impacts the input signature of the user function. | |
| - When used as an output, the component only impacts the return signature of the user function. | |
| The code snippet below is accurate in cases where the component is used as both an input and an output. | |
| ```python | |
| def predict( | |
| value: IGVContext | |
| ) -> IGVContext: | |
| return value | |
| ``` | |
| """, elem_classes=["md-custom", "IGV-user-fn"], header_links=True) | |
| code_IGVContext = gr.Markdown(""" | |
| ## `IGVContext` | |
| ```python | |
| class IGVContext(GradioModel): | |
| genome: str | ReferenceGenome = Field(default="hg38") | |
| locus: str = Field(default="") | |
| loadAlignmentTracks: list[AlignmentTrackLoad] = Field( | |
| default_factory=list | |
| ) | |
| loadVariantTracks: list[VariantTrackLoad] = Field( | |
| default_factory=list | |
| ) | |
| loadAnnotationTracks: list[AnnotationTrackLoad] = Field( | |
| default_factory=list | |
| ) | |
| removeTracks: list[str] = Field(default_factory=list) | |
| def update_genome(self, genome: str | ReferenceGenome): | |
| self.genome = genome | |
| return self | |
| def update_locus(self, locus: str): | |
| self.locus = locus | |
| return self | |
| def add_track(self, track_load: TrackLoad): | |
| if isinstance(track_load, AlignmentTrackLoad): | |
| self.loadAlignmentTracks.append(track_load) | |
| elif isinstance(track_load, VariantTrackLoad): | |
| self.loadVariantTracks.append(track_load) | |
| elif isinstance(track_load, AnnotationTrackLoad): | |
| self.loadAnnotationTracks.append(track_load) | |
| else: | |
| raise ValueError( | |
| "TrackLoad type not recognized." | |
| ) | |
| return self | |
| def remove_track(self, track: str): | |
| self.removeTracks.append(track) | |
| return self | |
| ```""", elem_classes=["md-custom", "IGVContext"], header_links=True) | |
| code_ReferenceGenome = gr.Markdown(""" | |
| ## `ReferenceGenome` | |
| ```python | |
| class ReferenceGenome(GradioModel): | |
| id: Optional[str] = Field(default="hg38") | |
| name: Optional[str] = Field(default="hg38") | |
| fastaURL: Optional[str] = Field(default=None) | |
| indexURL: Optional[str] = Field(default=None) | |
| compressedIndexURL: Optional[str] = Field(default=None) | |
| twoBitURL: Optional[str] = Field(default=None) | |
| cytobandURL: Optional[str] = Field(default=None) | |
| aliasURL: Optional[str] = Field(default=None) | |
| chromSizesURL: Optional[str] = Field(default=None) | |
| chromosomeOrder: Optional[list[str]] = Field( | |
| default=None | |
| ) | |
| headers: Optional[Dict[str, str]] = Field(default=None) | |
| wholeGenomeView: bool = Field(default=True) | |
| ```""", elem_classes=["md-custom", "ReferenceGenome"], header_links=True) | |
| code_AlignmentTrackLoad = gr.Markdown(""" | |
| ## `AlignmentTrackLoad` | |
| ```python | |
| class AlignmentTrackLoad(TrackLoad): | |
| showCoverage: bool = True | |
| showAlignments: bool = True | |
| viewAsPairs: bool = False | |
| pairsSupported: bool = True | |
| coverageColor: Optional[str] = None | |
| color: str = "rgb(170, 170, 170)" | |
| deletionColor: str = "black" | |
| displayMode: str = Field( | |
| default="EXPANDED", | |
| pattern="^(FULL|EXPANDED|SQUISHED)$", | |
| ) | |
| groupBy: Optional[str] = None | |
| samplingWindowSize: int = 100 | |
| samplingDepth: int = 100 | |
| readGroup: Optional[str] = None | |
| sort: Optional[AlignmentSortOptions] = None | |
| filter: Dict[str, bool | int | list[str]] = None | |
| showSoftClips: bool = False | |
| showMismatches: bool = True | |
| showAllBases: bool = False | |
| showInsertionText: bool = False | |
| insertionTextColor: str = "white" | |
| alignmentRowHeight: int = 14 | |
| squishedRowHeight: int = 3 | |
| colorBy: str = "unexpectedPair" | |
| insertionColor: str = "rgb(138, 94, 161)" | |
| negStrandColor: str = "rgba(150, 150, 230, 0.75)" | |
| ```""", elem_classes=["md-custom", "AlignmentTrackLoad"], header_links=True) | |
| code_AlignmentSortOptions = gr.Markdown(""" | |
| ## `AlignmentSortOptions` | |
| ```python | |
| class AlignmentSortOptions(GradioModel): | |
| chr: str | |
| position: int | |
| direction: Optional[str] = Field( | |
| default="ASC", pattern="^(ASC|DESC)$" | |
| ) | |
| option: str | |
| tag: Optional[str] = None | |
| ```""", elem_classes=["md-custom", "AlignmentSortOptions"], header_links=True) | |
| code_VariantTrackLoad = gr.Markdown(""" | |
| ## `VariantTrackLoad` | |
| ```python | |
| class VariantTrackLoad(TrackLoad): | |
| displayMode: Optional[str] = Field( | |
| default="EXPANDED", | |
| pattern="^(EXPANDED|SQUISHED|COLLAPSED)$", | |
| ) | |
| squishedCallHeight: Optional[int] = 1 | |
| expandedCallHeight: Optional[int] = 10 | |
| color: Optional[str] = None | |
| colorBy: Optional[str] = None | |
| colorTable: Optional[Dict[str, str]] = None | |
| noCallColor: Optional[str] = "rgb(250, 250, 250)" | |
| homvarColor: Optional[str] = "rgb(17,248,254)" | |
| hetvarColor: Optional[str] = "rgb(34,12,253)" | |
| homrefColor: Optional[str] = "rgb(200, 200, 200)" | |
| supportsWholeGenome: Optional[bool] = None | |
| showGenotypes: Optional[bool] = None | |
| # strokecolor: Optional[Callable[[VCFItem], str]] = None | |
| # context_hook: Optional[Callable[[VCFItem, Draw.CanvasContext, int, int, int, int], None]] = None | |
| ```""", elem_classes=["md-custom", "VariantTrackLoad"], header_links=True) | |
| code_AnnotationTrackLoad = gr.Markdown(""" | |
| ## `AnnotationTrackLoad` | |
| ```python | |
| class AnnotationTrackLoad(TrackLoad): | |
| displayMode: str = Field( | |
| default="COLLAPSED", | |
| pattern="^(EXPANDED|SQUISHED|COLLAPSED)$", | |
| ) | |
| squishedRowHeight: int = 15 | |
| expandedRowHeight: int = 30 | |
| color: str = "rgb(0,0,150)" | |
| colorBy: Optional[str] = None | |
| altColor: Optional[str] = None | |
| colorTable: Optional[Dict[str, str]] = None | |
| searchable: bool = False | |
| searchableFields: list[str] = Field( | |
| default_factory=list | |
| ) | |
| nameField: Optional[str] = None | |
| maxRows: int = 500 | |
| filterTypes: Optional[list[str]] = None | |
| ```""", elem_classes=["md-custom", "AnnotationTrackLoad"], header_links=True) | |
| demo.load(None, js=r"""function() { | |
| const refs = { | |
| IGVContext: ['ReferenceGenome', 'AlignmentTrackLoad', 'VariantTrackLoad', 'AnnotationTrackLoad'], | |
| ReferenceGenome: [], | |
| AlignmentTrackLoad: ['AlignmentSortOptions'], | |
| AlignmentSortOptions: [], | |
| VariantTrackLoad: [], | |
| AnnotationTrackLoad: [], }; | |
| const user_fn_refs = { | |
| IGV: ['IGVContext'], }; | |
| requestAnimationFrame(() => { | |
| Object.entries(user_fn_refs).forEach(([key, refs]) => { | |
| if (refs.length > 0) { | |
| const el = document.querySelector(`.${key}-user-fn`); | |
| if (!el) return; | |
| refs.forEach(ref => { | |
| el.innerHTML = el.innerHTML.replace( | |
| new RegExp("\\b"+ref+"\\b", "g"), | |
| `<a href="#h-${ref.toLowerCase()}">${ref}</a>` | |
| ); | |
| }) | |
| } | |
| }) | |
| Object.entries(refs).forEach(([key, refs]) => { | |
| if (refs.length > 0) { | |
| const el = document.querySelector(`.${key}`); | |
| if (!el) return; | |
| refs.forEach(ref => { | |
| el.innerHTML = el.innerHTML.replace( | |
| new RegExp("\\b"+ref+"\\b", "g"), | |
| `<a href="#h-${ref.toLowerCase()}">${ref}</a>` | |
| ); | |
| }) | |
| } | |
| }) | |
| }) | |
| } | |
| """) | |
| demo.launch() | |