28:null 29:["$","title",null,{"children":"PEQ Heatmap using PhamClust | WabushOnce | Observable"}] 2e:T1be6,phamclustCommandBuilder = { /* * These references are the actual control elements. * This cell does not directly depend on the reactive values * pathSettings, basicSettings, etc. */ const pathControl = viewof pathSettings; const basicControl = viewof basicSettings; const clusterControl = viewof clusterSettings; const subclusterControl = viewof subclusterSettings; const heatmapControl = viewof heatmapSettings; const runInfoControl = viewof runInformation; const textarea = html` `; const copyButton = html` `; const downloadSlot = html` `; const controlsPanel = html`

PhamClust settings

${pathControl} ${basicControl} ${clusterControl} ${subclusterControl} ${heatmapControl} ${runInfoControl}

`; const container = html`

Configure and run PhamClust

${controlsPanel}

Generated WSL code

Copy the complete script, paste it into WSL, and press Enter.

${textarea}

${copyButton} ${downloadSlot}

`; const controls = [ pathControl, basicControl, clusterControl, subclusterControl, heatmapControl, runInfoControl ]; let currentScript = ""; function controlValue(control) { return control?.value ?? {}; } function updateDownloadButton() { const downloadButton = DOM.download( new Blob([currentScript], { type: "text/x-shellscript;charset=utf-8" }), "run_phamclust.sh", "⬇ Download run_phamclust.sh" ); downloadSlot.replaceChildren(downloadButton); } function generateScript() { /* * Reading .value directly does not cause the Observable cell * to be reconstructed. */ currentScript = buildPhamclustScript({ pathSettings: controlValue(pathControl), basicSettings: controlValue(basicControl), clusterSettings: controlValue(clusterControl), subclusterSettings: controlValue(subclusterControl), heatmapSettings: controlValue(heatmapControl), runInformation: controlValue(runInfoControl) }); textarea.value = currentScript; updateDownloadButton(); } const handleControlInput = () => { /* * Only the generated text changes. * The focused input remains the same mounted DOM element. */ generateScript(); }; for (const control of controls) { control.addEventListener("input", handleControlInput); } copyButton.onclick = async () => { try { await navigator.clipboard.writeText(currentScript); copyButton.textContent = "✅ Copied!"; setTimeout(() => { copyButton.textContent = "📋 Copy PhamClust WSL code"; }, 1500); } catch (error) { textarea.focus(); textarea.select(); copyButton.textContent = "Select the code and press Ctrl+C"; setTimeout(() => { copyButton.textContent = "📋 Copy PhamClust WSL code"; }, 2500); } }; function matchTextareaHeight() { requestAnimationFrame(() => { const height = controlsPanel.getBoundingClientRect().height; if (height > 0) { textarea.style.height = `${Math.round(height)}px`; } }); } const resizeObserver = new ResizeObserver(matchTextareaHeight); resizeObserver.observe(controlsPanel); const handleToggle = (event) => { if (event.target === container && container.open) { matchTextareaHeight(); } }; const handleWindowResize = () => { matchTextareaHeight(); }; container.addEventListener("toggle", handleToggle); window.addEventListener("resize", handleWindowResize); invalidation.then(() => { resizeObserver.disconnect(); for (const control of controls) { control.removeEventListener("input", handleControlInput); } container.removeEventListener("toggle", handleToggle); window.removeEventListener("resize", handleWindowResize); }); generateScript(); matchTextareaHeight(); return container; }2f:T12ad,phamclustFigureLegend = { const metricLabels = { peq: "proteomic equivalence quotient (PEQ)", gcs: "gene content similarity (GCS)", jc: "Jaccard coefficient", pocp: "percentage of conserved proteins (POCP)", af: "alignment fraction", aai: "average amino acid identity (AAI)" }; const metric = String(basicSettings?.metric ?? "peq") .trim() .toLowerCase(); const metricName = metricLabels[metric] ?? String(basicSettings?.metric ?? "PEQ"); const clusterThreshold = Number(clusterSettings?.clusterThreshold ?? 0.25); const clusterLinkage = String( clusterSettings?.clusterLinkage ?? "average" ).trim(); const subclusteringEnabled = Boolean(basicSettings?.performSubclustering); const subclusterThreshold = Number( subclusterSettings?.subclusterThreshold ?? 0.6 ); const subclusterLinkage = String( subclusterSettings?.subclusterLinkage ?? "single" ).trim(); const minimumClusterSize = Math.round( Number(subclusterSettings?.minimumClusterSize ?? 6) ); const lowColor = String(heatmapSettings?.lowColor ?? "red").trim(); const middleColor = String(heatmapSettings?.middleColor ?? "yellow").trim(); const highColor = String(heatmapSettings?.highColor ?? "green").trim(); const colorDescription = middleColor ? `${lowColor} indicates lower similarity, ${middleColor} indicates intermediate similarity, and ${highColor} indicates higher similarity` : `${lowColor} indicates lower similarity and ${highColor} indicates higher similarity`; const subclusterSentence = subclusteringEnabled ? ` Main clusters containing at least ${minimumClusterSize} genomes were evaluated for subclustering using ${subclusterLinkage}-linkage clustering at a similarity threshold of ${subclusterThreshold}.` : " Subclustering was not performed."; const legend = `Figure X. PhamClust heatmap showing pairwise ${metricName} among the selected bacteriophage genomes. ` + `Each row and column represents one phage genome, and heatmap colours indicate the degree of pairwise similarity; ${colorDescription}. ` + `Genomes were grouped using ${clusterLinkage}-linkage hierarchical clustering with a main-cluster similarity threshold of ${clusterThreshold}.` + subclusterSentence; const textarea = html` `; textarea.value = legend; const copyButton = html` `; copyButton.onclick = async () => { try { await navigator.clipboard.writeText(legend); copyButton.textContent = "✅ Legend copied"; setTimeout(() => { copyButton.textContent = "📋 Copy figure legend"; }, 1500); } catch (error) { textarea.focus(); textarea.select(); copyButton.textContent = "Select the legend and press Ctrl+C"; setTimeout(() => { copyButton.textContent = "📋 Copy figure legend"; }, 2500); } }; return html`

PhamClust figure legend

The legend updates automatically when the PhamClust parameters change.

${textarea}

${copyButton}

`; }30:T4716,viewof resultsTable = { /* * Keep the complete phage metadata array in memory, but never render * every phage at once. Only phages from the selected cluster/subcluster * are shown in the Available panel. */ const allRows = (availablePhageRows ?? []) .filter((d) => d?.phage_name) .slice() .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)); const MAX_VISIBLE = 250; const UNCLUSTERED = "__UNCLUSTERED__"; /* * This set persists while the user switches clusters and subclusters * within this interface. */ const selectedNames = new Set(); let searchTerm = ""; const buttonStyle = ` padding:7px 11px; border:1px solid #c7cdd4; border-radius:7px; background:white; cursor:pointer; font:12px sans-serif; white-space:nowrap; `; const selectStyle = ` box-sizing:border-box; width:100%; border:1px solid #c7cdd4; border-radius:8px; background:white; font:12px sans-serif; `; const wrap = html`

Select phages for the PhamClust TSV

Available phages

Cluster Subcluster

Search within the selected cluster

Selected phages

Search selected list

`; const overallSummary = wrap.querySelector(".overall-summary"); const clearAllButton = wrap.querySelector(".clear-all-button"); const clusterSelect = wrap.querySelector(".cluster-select"); const subclusterSelect = wrap.querySelector(".subcluster-select"); const availableSearch = wrap.querySelector(".available-search"); const availableSummary = wrap.querySelector(".available-summary"); const availableList = wrap.querySelector(".available-list"); const addCheckedButton = wrap.querySelector(".add-checked-button"); const addVisibleButton = wrap.querySelector(".add-visible-button"); const addAnnotatedButton = wrap.querySelector(".add-annotated-button"); const selectedSearch = wrap.querySelector(".selected-search"); const selectedSummary = wrap.querySelector(".selected-summary"); const selectedCount = wrap.querySelector(".selected-count"); const selectedList = wrap.querySelector(".selected-list"); const removeCheckedButton = wrap.querySelector(".remove-checked-button"); const removeVisibleButton = wrap.querySelector(".remove-visible-button"); function clusterValue(row) { const value = String(row.cluster ?? "").trim(); return value || UNCLUSTERED; } function clusterLabel(value) { return value === UNCLUSTERED ? "(Unclustered)" : value; } function subclusterValue(row) { return String(row.subcluster ?? "").trim(); } function isDraftPhage(row) { return /_Draft$/i.test(String(row.phage_name ?? "").trim()); } function setOptions( select, values, { placeholder = null, label = (value) => value, selectedValue = "" } = {} ) { select.replaceChildren(); if (placeholder !== null) { const option = document.createElement("option"); option.value = ""; option.textContent = placeholder; option.selected = !selectedValue; select.append(option); } for (const value of values) { const option = document.createElement("option"); option.value = value; option.textContent = label(value); option.selected = value === selectedValue; select.append(option); } } function selectedOptionValues(select) { return [...select.selectedOptions] .map((option) => option.value) .filter(Boolean); } const clusters = [...new Set(allRows.map(clusterValue))].sort((a, b) => { if (a === UNCLUSTERED) return 1; if (b === UNCLUSTERED) return -1; return d3.ascending(a, b); }); setOptions(clusterSelect, clusters, { placeholder: "Choose a cluster", label: clusterLabel }); setOptions(subclusterSelect, [], { placeholder: "All subclusters" }); function rowsForSelectedCluster() { const cluster = clusterSelect.value; if (!cluster) return []; return allRows.filter((row) => clusterValue(row) === cluster); } function updateSubclusterOptions() { const currentCluster = clusterSelect.value; const previousValue = subclusterSelect.value; if (!currentCluster) { subclusterSelect.disabled = true; setOptions(subclusterSelect, [], { placeholder: "All subclusters" }); return; } const subclusters = [ ...new Set(rowsForSelectedCluster().map(subclusterValue).filter(Boolean)) ].sort(d3.ascending); const retainedValue = subclusters.includes(previousValue) ? previousValue : ""; setOptions(subclusterSelect, subclusters, { placeholder: "All subclusters", selectedValue: retainedValue }); subclusterSelect.disabled = subclusters.length === 0; } function matchingAvailableRows() { const cluster = clusterSelect.value; if (!cluster) return []; const subcluster = subclusterSelect.value; const query = searchTerm.trim().toLowerCase(); return rowsForSelectedCluster() .filter((row) => !subcluster || subclusterValue(row) === subcluster) .filter((row) => !query || row.phage_name.toLowerCase().includes(query)) .filter((row) => !selectedNames.has(row.phage_name)) .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)); } /* * These are the annotated phages currently available under the * selected cluster, subcluster, and name-search filters. * * Phages already in the Selected list have already been removed * by matchingAvailableRows(). */ function matchingAnnotatedRows() { return matchingAvailableRows().filter((row) => !isDraftPhage(row)); } function matchingSelectedRows() { const query = selectedSearch.value.trim().toLowerCase(); return allRows .filter((row) => selectedNames.has(row.phage_name)) .filter( (row) => !query || row.phage_name.toLowerCase().includes(query) || String(row.cluster ?? "") .toLowerCase() .includes(query) || String(row.subcluster ?? "") .toLowerCase() .includes(query) ) .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)); } function makePhageOption(row) { const option = document.createElement("option"); option.value = row.phage_name; option.textContent = row.phage_name; return option; } function updateOutputValue() { const selectedRows = allRows .filter((row) => selectedNames.has(row.phage_name)) .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)); wrap.value = { selectedRows, selectedPhageNames: selectedRows.map((row) => row.phage_name), selectedCount: selectedRows.length }; wrap.dispatchEvent( new CustomEvent("input", { bubbles: true }) ); } function renderAvailable() { const matching = matchingAvailableRows(); const annotated = matchingAnnotatedRows(); const visible = matching.slice(0, MAX_VISIBLE); availableList.replaceChildren(...visible.map(makePhageOption)); if (!clusterSelect.value) { availableSummary.textContent = "Choose a cluster to list its phages."; } else if (!matching.length) { availableSummary.textContent = "No unselected phages match the current filters."; } else if (matching.length > MAX_VISIBLE) { availableSummary.textContent = `Showing ${MAX_VISIBLE} of ${matching.length} matches. ` + "Refine the subcluster or search to narrow the list."; } else { availableSummary.textContent = `${matching.length} matching phage` + `${matching.length === 1 ? "" : "s"}.`; } addCheckedButton.disabled = visible.length === 0; addVisibleButton.disabled = matching.length === 0; addAnnotatedButton.disabled = annotated.length === 0; addAnnotatedButton.textContent = annotated.length > 0 ? `Add Annotated (${annotated.length})` : "Add Annotated"; } function renderSelected() { const shown = matchingSelectedRows(); selectedList.replaceChildren(...shown.map(makePhageOption)); selectedCount.textContent = `${selectedNames.size} selected`; selectedSummary.textContent = shown.length === selectedNames.size ? `${shown.length} phage` + `${shown.length === 1 ? "" : "s"} shown.` : `Showing ${shown.length} of ` + `${selectedNames.size} selected phages.`; removeCheckedButton.disabled = shown.length === 0; removeVisibleButton.disabled = shown.length === 0; clearAllButton.disabled = selectedNames.size === 0; overallSummary.textContent = `${allRows.length.toLocaleString()} phages available; ` + `${selectedNames.size.toLocaleString()} selected.`; } function renderAll() { renderAvailable(); renderSelected(); updateOutputValue(); } clusterSelect.onchange = () => { searchTerm = ""; availableSearch.value = ""; updateSubclusterOptions(); renderAvailable(); }; subclusterSelect.onchange = () => { renderAvailable(); }; availableSearch.oninput = () => { searchTerm = availableSearch.value; renderAvailable(); }; selectedSearch.oninput = () => { renderSelected(); }; addCheckedButton.onclick = () => { for (const name of selectedOptionValues(availableList)) { selectedNames.add(name); } renderAll(); }; addVisibleButton.onclick = () => { /* * Add every current match, including matches beyond the * first 250 entries displayed in the list. */ for (const row of matchingAvailableRows()) { selectedNames.add(row.phage_name); } renderAll(); }; addAnnotatedButton.onclick = () => { /* * Add only annotated phages from the current Available result set. * * This respects: * - the selected cluster; * - the selected subcluster; * - the current name search; * - phages already selected; * - the exclusion of names ending in "_Draft". */ for (const row of matchingAnnotatedRows()) { selectedNames.add(row.phage_name); } renderAll(); }; removeCheckedButton.onclick = () => { for (const name of selectedOptionValues(selectedList)) { selectedNames.delete(name); } renderAll(); }; removeVisibleButton.onclick = () => { for (const row of matchingSelectedRows()) { selectedNames.delete(row.phage_name); } renderAll(); }; clearAllButton.onclick = () => { selectedNames.clear(); selectedSearch.value = ""; renderAll(); }; /* * Double-clicking moves one phage between panels. */ availableList.ondblclick = () => { const name = availableList.value; if (name) { selectedNames.add(name); renderAll(); } }; selectedList.ondblclick = () => { const name = selectedList.value; if (name) { selectedNames.delete(name); renderAll(); } }; updateSubclusterOptions(); renderAll(); return wrap; }31:Tb1b,{ const v = phamclustValidation; const ready = v.requestedPhages > 0 && v.exportableGenes > 0 && v.requestErrors.length === 0; return html`

${ready ? "✅ PhamClust TSV is ready" : "ℹ️ TSV validation summary"}

Requested phages: ${v.requestedPhages}

Phages returned: ${v.returnedPhages}

Source genes: ${v.sourceGenes}

Exportable genes: ${v.exportableGenes}

Unique phams: ${v.uniquePhams}

Missing pham: ${v.missingPham}

Missing translation: ${v.missingTranslation}

Invalid translation: ${v.invalidTranslation}

Request errors: ${v.requestErrors.length}

${ v.phagesWithNoGenes.length ? html`

Phages with no returned genes (${v.phagesWithNoGenes.length})

                  ${v.phagesWithNoGenes.join(", ")}
                

` : "" } ${ v.requestErrors.length ? html`

API request errors (${v.requestErrors.length})

${v.requestErrors
                  .map(
                    (d) =>
                      `${d.phageName}: ${d.message}`
                  )
                  .join("\n")}

` : "" }

`; }32:T5ca,{ const previewRows = (phamclustRows ?? []).slice(0, 25); const textarea = html` `; textarea.value = previewRows.length ? previewRows .map((d) => [ d.phage_name, d.pham, d.translation ].join("\t") ) .join("\n") : "Select phages and retrieve their genes to create a preview."; return html`

TSV preview ${ previewRows.length ? `(first ${previewRows.length} rows)` : "" }

The exported file has no header row.

${textarea}

`; } 33:T3400,viewof phamclustInstaller = { // ------------------------------------------------------------ // Controls // ------------------------------------------------------------ const environmentNameInput = Inputs.text({ label: "🧪 Conda environment name", value: "phamclust", placeholder: "phamclust", style: "width: 100%;" }); const pythonVersionInput = Inputs.select(["3.11", "3.12", "3.10"], { label: "🐍 Python version", value: "3.11" }); const installationSourceInput = Inputs.select( ["GitHub — latest repository version", "PyPI — latest published release"], { label: "📦 PhamClust installation source", value: "PyPI — latest published release" } ); const recreateEnvironmentInput = Inputs.toggle({ label: "Remove and recreate the environment if it already exists", value: false }); const updatePipInput = Inputs.toggle({ label: "Update pip, setuptools, and wheel", value: true }); const installGitInput = Inputs.toggle({ label: "Install Git in the Conda environment", value: true }); const runVerificationInput = Inputs.toggle({ label: "Run PhamClust verification after installation", value: true }); // ------------------------------------------------------------ // Generated-code textarea // ------------------------------------------------------------ const textarea = html` `; const copyButton = html` `; // ------------------------------------------------------------ // Helpers // ------------------------------------------------------------ function shellQuote(value) { return `'${String(value ?? "").replace(/'/g, `'\\''`)}'`; } function getInputValue(input) { return input.value; } // ------------------------------------------------------------ // Generate the WSL installer // ------------------------------------------------------------ function generateScript() { const environmentName = String(getInputValue(environmentNameInput) ?? "").trim() || "phamclust"; const pythonVersion = String(getInputValue(pythonVersionInput) ?? "").trim() || "3.11"; const installationSource = getInputValue(installationSourceInput); const recreateEnvironment = Boolean( getInputValue(recreateEnvironmentInput) ); const updatePip = Boolean(getInputValue(updatePipInput)); const installGit = Boolean(getInputValue(installGitInput)); const runVerification = Boolean(getInputValue(runVerificationInput)); const installTarget = installationSource === "PyPI — latest published release" ? "phamclust" : "git+https://github.com/chg60/phamclust.git"; const condaPackages = [ `"python=$PYTHON_VERSION"`, ...(installGit ? ["git"] : []), "pip" ]; const recreateBlock = recreateEnvironment ? ` echo "🔎 Checking whether the environment already exists..." if conda env list | awk '{print $1}' | grep -Fxq "$ENV_NAME"; then echo "🗑️ Removing existing environment: $ENV_NAME" conda deactivate 2>/dev/null || true conda env remove --name "$ENV_NAME" --yes fi ` : ""; const updatePipBlock = updatePip ? ` echo "⬆️ Updating pip, setuptools, and wheel..." python -m pip install --upgrade pip setuptools wheel ` : ""; const verificationBlock = runVerification ? ` echo echo "🧪 Verifying the PhamClust installation..." if ! command -v phamclust >/dev/null 2>&1; then echo "❌ The phamclust executable was not found after installation." exit 1 fi echo "PhamClust executable:" command -v phamclust echo echo "PhamClust version:" python -c "from importlib.metadata import version; print(version('phamclust'))" echo echo "PhamClust help:" phamclust --help echo echo "✅ PhamClust was installed successfully." ` : ` echo echo "✅ PhamClust installation completed." `; const innerScript = `#!/usr/bin/env bash set -Eeuo pipefail trap 'status=$?; echo; echo "❌ PhamClust installation failed at line $LINENO (exit $status)"; exit $status' ERR export PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:\${PATH:-}" ENV_NAME=${shellQuote(environmentName)} PYTHON_VERSION=${shellQuote(pythonVersion)} INSTALL_TARGET=${shellQuote(installTarget)} echo "============================================================" echo " PhamClust WSL installer" echo "============================================================" echo echo "🧪 Conda environment: $ENV_NAME" echo "🐍 Python version: $PYTHON_VERSION" echo "📦 Installation: $INSTALL_TARGET" echo # ------------------------------------------------------------ # Locate and initialize Conda # ------------------------------------------------------------ if command -v conda >/dev/null 2>&1; then CONDA_BASE="$(conda info --base)" elif [ -f "$HOME/miniconda/bin/conda" ]; then CONDA_BASE="$HOME/miniconda" elif [ -f "$HOME/miniconda3/bin/conda" ]; then CONDA_BASE="$HOME/miniconda3" elif [ -f "$HOME/miniforge3/bin/conda" ]; then CONDA_BASE="$HOME/miniforge3" else echo "❌ Conda was not found." echo echo "Install Miniconda, Miniforge, or Anaconda in WSL first." exit 1 fi if [ ! -f "$CONDA_BASE/etc/profile.d/conda.sh" ]; then echo "❌ Could not find:" echo " $CONDA_BASE/etc/profile.d/conda.sh" exit 1 fi font source "$CONDA_BASE/etc/profile.d/conda.sh" echo "📦 Conda installation:" echo " $CONDA_BASE" ${recreateBlock} # ------------------------------------------------------------ # Create or reuse the environment # ------------------------------------------------------------ if conda env list | awk '{print $1}' | grep -Fxq "$ENV_NAME"; then echo "ℹ️ Conda environment already exists: $ENV_NAME" else echo "🛠️ Creating Conda environment: $ENV_NAME" conda create \\ --name "$ENV_NAME" \\ ${condaPackages.join(" \\\n ")} \\ --yes fi echo echo "🧪 Activating environment: $ENV_NAME" conda activate "$ENV_NAME" if [ -z "\${CONDA_PREFIX:-}" ]; then echo "❌ CONDA_PREFIX is empty after environment activation." exit 1 fi echo "📁 Active environment path:" echo " $CONDA_PREFIX" echo echo "🐍 Python executable:" command -v python echo python --version ${updatePipBlock} # ------------------------------------------------------------ # Install or update PhamClust # ------------------------------------------------------------ echo echo "⬇️ Installing/updating PhamClust..." python -m pip install --upgrade "$INSTALL_TARGET" ${verificationBlock} echo echo "To use PhamClust later, run:" echo echo " conda activate $ENV_NAME" echo " phamclust --help" `; textarea.value = `bash <<'PHAMCLUST_INSTALLER' ${innerScript} PHAMCLUST_INSTALLER`; container.value = { environmentName, pythonVersion, installationSource, recreateEnvironment, updatePip, installGit, runVerification, script: textarea.value }; container.dispatchEvent( new CustomEvent("input", { bubbles: true }) ); } // ------------------------------------------------------------ // Copy button // ------------------------------------------------------------ copyButton.onclick = async () => { try { await navigator.clipboard.writeText(textarea.value); copyButton.textContent = "✅ Copied!"; setTimeout(() => { copyButton.textContent = "📋 Copy PhamClust installer"; }, 1500); } catch (error) { textarea.focus(); textarea.select(); copyButton.textContent = "Select the code and press Ctrl+C"; setTimeout(() => { copyButton.textContent = "📋 Copy PhamClust installer"; }, 2500); } }; // ------------------------------------------------------------ // Controls panel // ------------------------------------------------------------ const controlsPanel = html`

Installation settings

${environmentNameInput} ${pythonVersionInput} ${installationSourceInput} ${recreateEnvironmentInput} ${updatePipInput} ${installGitInput} ${runVerificationInput}

`; // ------------------------------------------------------------ // Layout // ------------------------------------------------------------ const container = html`

Install or update PhamClust

${controlsPanel}

Generated WSL installation code

Copy the complete generated block, paste it directly into WSL, and press Enter.

${textarea}

${copyButton}

`; // ------------------------------------------------------------ // Match textarea height to the controls panel // ------------------------------------------------------------ function matchTextareaHeight() { requestAnimationFrame(() => { const controlsHeight = controlsPanel.getBoundingClientRect().height; if (controlsHeight > 0) { textarea.style.height = `${Math.round(controlsHeight)}px`; } }); } // Watch the controls panel in case its height changes. const resizeObserver = new ResizeObserver(() => { matchTextareaHeight(); }); resizeObserver.observe(controlsPanel); // Recalculate when the collapsible section is opened. container.addEventListener("toggle", (event) => { if (event.target.open) { matchTextareaHeight(); } }); // Recalculate when the browser or notebook width changes. window.addEventListener("resize", matchTextareaHeight); // ------------------------------------------------------------ // React to control changes // ------------------------------------------------------------ [ environmentNameInput, pythonVersionInput, installationSourceInput, recreateEnvironmentInput, updatePipInput, installGitInput, runVerificationInput ].forEach((input) => { input.addEventListener("input", () => { generateScript(); matchTextareaHeight(); }); input.addEventListener("change", () => { generateScript(); matchTextareaHeight(); }); }); generateScript(); matchTextareaHeight(); return container; }34:T39dd,viewof heatmapSettings = { const cssColorNames = [ "aliceblue", "antiquewhite", "aqua", "aquamarine", "azure", "beige", "bisque", "black", "blanchedalmond", "blue", "blueviolet", "brown", "burlywood", "cadetblue", "chartreuse", "chocolate", "coral", "cornflowerblue", "cornsilk", "crimson", "cyan", "darkblue", "darkcyan", "darkgoldenrod", "darkgray", "darkgrey", "darkgreen", "darkkhaki", "darkmagenta", "darkolivegreen", "darkorange", "darkorchid", "darkred", "darksalmon", "darkseagreen", "darkslateblue", "darkslategray", "darkslategrey", "darkturquoise", "darkviolet", "deeppink", "deepskyblue", "dimgray", "dimgrey", "dodgerblue", "firebrick", "floralwhite", "forestgreen", "fuchsia", "gainsboro", "ghostwhite", "gold", "goldenrod", "gray", "grey", "green", "greenyellow", "honeydew", "hotpink", "indianred", "indigo", "ivory", "khaki", "lavender", "lavenderblush", "lawngreen", "lemonchiffon", "lightblue", "lightcoral", "lightcyan", "lightgoldenrodyellow", "lightgray", "lightgrey", "lightgreen", "lightpink", "lightsalmon", "lightseagreen", "lightskyblue", "lightslategray", "lightslategrey", "lightsteelblue", "lightyellow", "lime", "limegreen", "linen", "magenta", "maroon", "mediumaquamarine", "mediumblue", "mediumorchid", "mediumpurple", "mediumseagreen", "mediumslateblue", "mediumspringgreen", "mediumturquoise", "mediumvioletred", "midnightblue", "mintcream", "mistyrose", "moccasin", "navajowhite", "navy", "oldlace", "olive", "olivedrab", "orange", "orangered", "orchid", "palegoldenrod", "palegreen", "paleturquoise", "palevioletred", "papayawhip", "peachpuff", "peru", "pink", "plum", "powderblue", "purple", "red", "rosybrown", "royalblue", "saddlebrown", "salmon", "sandybrown", "seagreen", "seashell", "sienna", "silver", "skyblue", "slateblue", "slategray", "slategrey", "snow", "springgreen", "steelblue", "tan", "teal", "thistle", "tomato", "turquoise", "violet", "wheat", "white", "whitesmoke", "yellow", "yellowgreen" ]; const colorNameSet = new Set(cssColorNames); const buttonStyle = ` padding:7px 10px; border:1px solid #c7cdd4; border-radius:7px; background:white; cursor:pointer; font:12px sans-serif; white-space:nowrap; `; const inputStyle = ` box-sizing:border-box; width:100%; padding:7px 9px; border:1px solid #c7cdd4; border-radius:7px; background:white; font:13px sans-serif; `; const container = html`

Heatmap settings

Heatmap color gradient

Heatmap midpoint

`; const gradientMode = container.querySelector(".gradient-mode"); const colorControls = container.querySelector(".color-controls"); const palettePanel = container.querySelector(".palette-panel"); const midpointInput = container.querySelector(".heatmap-midpoint"); const gradientPreview = container.querySelector(".gradient-preview"); const validationMessage = container.querySelector(".validation-message"); const swatchGrid = container.querySelector(".swatch-grid"); const closePaletteButton = container.querySelector(".close-palette"); const paletteTargetLabel = container.querySelector(".palette-target-label"); let activeColorControl = null; function makeColorControl( key, label, defaultValue ) { const row = html`

${label}

`; colorControls.append(row); const control = { key, label, row, input: row.querySelector(`.${key}-input`), swatch: row.querySelector(`.${key}-swatch`), button: row.querySelector(`.${key}-choose`) }; control.button.onclick = () => { activeColorControl = control; paletteTargetLabel.textContent = `Selecting: ${label}`; palettePanel.style.display = "block"; requestAnimationFrame(() => { palettePanel.scrollIntoView({ behavior: "smooth", block: "nearest" }); }); }; return control; } const lowControl = makeColorControl( "low-color", "Low-similarity color", "red" ); const middleControl = makeColorControl( "middle-color", "Middle-similarity color", "yellow" ); const highControl = makeColorControl( "high-color", "High-similarity color", "green" ); function normalizedColor(control) { return String(control.input.value ?? "") .trim() .toLowerCase(); } function updateSwatch(control) { const color = normalizedColor(control); const valid = colorNameSet.has(color); control.swatch.style.background = valid ? color : "transparent"; control.swatch.title = valid ? color : "Invalid color"; return valid; } function cssColorToRgb(colorName) { const probe = document.createElement("span"); probe.style.color = colorName; probe.style.display = "none"; document.body.append(probe); const computed = getComputedStyle(probe).color; probe.remove(); const match = computed.match( /rgba?\(\s*(\d+),\s*(\d+),\s*(\d+)/ ); if (!match) { return { red: 0, green: 0, blue: 0 }; } return { red: Number(match[1]), green: Number(match[2]), blue: Number(match[3]) }; } function rgbToHsl(red, green, blue) { const r = red / 255; const g = green / 255; const b = blue / 255; const maximum = Math.max(r, g, b); const minimum = Math.min(r, g, b); const difference = maximum - minimum; let hue = 0; if (difference !== 0) { if (maximum === r) { hue = 60 * (((g - b) / difference) % 6); } else if (maximum === g) { hue = 60 * ((b - r) / difference + 2); } else { hue = 60 * ((r - g) / difference + 4); } } if (hue < 0) { hue += 360; } const lightness = (maximum + minimum) / 2; const saturation = difference === 0 ? 0 : difference / ( 1 - Math.abs(2 * lightness - 1) ); return { hue, saturation, lightness }; } const sortedCssColorNames = cssColorNames .map((name) => { const rgb = cssColorToRgb(name); const hsl = rgbToHsl( rgb.red, rgb.green, rgb.blue ); return { name, hue: hsl.hue, saturation: hsl.saturation, lightness: hsl.lightness }; }) .sort((a, b) => { const aNeutral = a.saturation < 0.08; const bNeutral = b.saturation < 0.08; if (aNeutral !== bNeutral) { return aNeutral ? 1 : -1; } if (aNeutral && bNeutral) { return ( a.lightness - b.lightness ); } return ( a.hue - b.hue || a.lightness - b.lightness || b.saturation - a.saturation ); }) .map((d) => d.name); function closePalette() { palettePanel.style.display = "none"; activeColorControl = null; } function chooseColor(colorName) { if (!activeColorControl) { return; } activeColorControl.input.value = colorName; updateValue(); closePalette(); } function renderPalette() { swatchGrid.replaceChildren( ...sortedCssColorNames.map( (colorName) => { const button = html` `; button.onclick = () => { chooseColor(colorName); }; return button; } ) ); } function updateValue() { const useMiddle = gradientMode.value === "Three-color gradient"; middleControl.row.style.display = useMiddle ? "grid" : "none"; const lowValid = updateSwatch(lowControl); const middleValid = !useMiddle || updateSwatch(middleControl); const highValid = updateSwatch(highControl); const invalid = []; if (!lowValid) { invalid.push("low-similarity color"); } if (!middleValid) { invalid.push("middle-similarity color"); } if (!highValid) { invalid.push("high-similarity color"); } validationMessage.textContent = invalid.length ? `Choose a supported color for: ${invalid.join(", ")}.` : ""; const lowColor = normalizedColor(lowControl); const middleColor = normalizedColor(middleControl); const highColor = normalizedColor(highControl); const colors = useMiddle ? [ lowColor, middleColor, highColor ] : [ lowColor, highColor ]; gradientPreview.style.background = invalid.length === 0 ? `linear-gradient( to right, ${colors.join(", ")} )` : "transparent"; container.value = { gradientMode: gradientMode.value, lowColor, middleColor: useMiddle ? middleColor : "", highColor, heatmapMidpoint: Number(midpointInput.value), colorsValid: invalid.length === 0 }; container.dispatchEvent( new CustomEvent("input", { bubbles: true }) ); } gradientMode.addEventListener( "change", () => { closePalette(); updateValue(); } ); midpointInput.addEventListener( "input", updateValue ); midpointInput.addEventListener( "change", updateValue ); closePaletteButton.onclick = closePalette; renderPalette(); updateValue(); return container; }35:T54c,validationMessages = { const messages = []; if (!String(pathSettings.environmentName ?? "").trim()) { messages.push("Enter a Conda environment name."); } if (!resolvedPaths.input) { messages.push("Enter an input path."); } if (!resolvedPaths.output) { messages.push("Enter an output directory."); } if ( Number(clusterSettings.clusterThreshold) < 0 || Number(clusterSettings.clusterThreshold) > 1 ) { messages.push( "The main clustering threshold must be between 0 and 1." ); } if ( Number(clusterSettings.nonredundantThreshold) < 0 || Number(clusterSettings.nonredundantThreshold) > 1 ) { messages.push( "The pre-grouping threshold must be between 0 and 1." ); } if ( basicSettings.performSubclustering && ( Number(subclusterSettings.subclusterThreshold) < 0 || Number(subclusterSettings.subclusterThreshold) > 1 ) ) { messages.push( "The subclustering threshold must be between 0 and 1." ); } if (heatmapSettings.useCustomHeatmapColors) { if (!String(heatmapSettings.lowColor ?? "").trim()) { messages.push("Enter a low-similarity heatmap color."); } if (!String(heatmapSettings.highColor ?? "").trim()) { messages.push("Enter a high-similarity heatmap color."); } } return messages; }36:T2b32,buildPhamclustScript = ({ pathSettings, basicSettings, clusterSettings, subclusterSettings, heatmapSettings, runInformation }) => { function shQuote(value) { return `'${String(value ?? "").replace( /'/g, `'\\''` )}'`; } function windowsToWSLPath(path) { let value = String(path ?? "") .trim() .replace(/^["']|["']$/g, ""); if (!value) { return ""; } // Leave valid WSL/Linux paths unchanged. if (/^\/mnt\/[a-z]\//i.test(value)) { return value.replace(/\\/g, "/"); } if (value.startsWith("/")) { return value; } // Reject malformed text containing multiple Windows paths. const driveMatches = value.match(/[A-Za-z]:[\\/]/g) ?? []; if (driveMatches.length > 1) { throw new Error( `The path contains more than one Windows path: ${value}` ); } // Convert C:\Folder\File or C:/Folder/File. const match = value.match( /^([A-Za-z]):[\\/](.*)$/ ); if (!match) { throw new Error( `Invalid Windows path: ${value}` ); } const drive = match[1].toLowerCase(); const remainder = match[2] .replace(/\\/g, "/") .replace(/^\/+/, "") .replace(/\/+/g, "/"); return `/mnt/${drive}/${remainder}`; } function finiteNumber( value, fallback, minimum = -Infinity, maximum = Infinity ) { const number = Number(value); if (!Number.isFinite(number)) { return fallback; } return Math.min( maximum, Math.max(minimum, number) ); } function positiveInteger(value, fallback) { const number = Math.round(Number(value)); return Number.isFinite(number) && number >= 1 ? number : fallback; } // ---------------------------------------------------------- // Paths // ---------------------------------------------------------- const rawInputPath = String( pathSettings?.inputPath ?? "" ).trim(); const rawOutputDirectory = String( pathSettings?.outputDirectory ?? "" ).trim(); const convertWindowsPaths = String(pathSettings?.pathStyle ?? "") === "Windows paths — convert automatically to WSL"; const inputPath = convertWindowsPaths ? windowsToWSLPath(rawInputPath) : rawInputPath; const outputDirectory = convertWindowsPaths ? windowsToWSLPath(rawOutputDirectory) : rawOutputDirectory; if ( convertWindowsPaths && inputPath && !/^\/mnt\/[a-z]\//i.test(inputPath) ) { throw new Error( `Input path was not converted correctly: ${inputPath}` ); } if ( convertWindowsPaths && outputDirectory && !/^\/mnt\/[a-z]\//i.test(outputDirectory) ) { throw new Error( `Output path was not converted correctly: ${outputDirectory}` ); } // ---------------------------------------------------------- // Basic settings // ---------------------------------------------------------- const environmentName = String( basicSettings?.environmentName ?? basicSettings?.envName ?? "phamclust" ).trim() || "phamclust"; const metric = String( basicSettings?.metric ?? "peq" ) .trim() .toLowerCase() || "peq"; const threads = positiveInteger( basicSettings?.threads, 4 ); // ---------------------------------------------------------- // Main clustering and pre-grouping // ---------------------------------------------------------- const clusterThreshold = finiteNumber( clusterSettings?.clusterThreshold, 0.25, 0, 1 ); const clusterLinkage = String( clusterSettings?.clusterLinkage ?? "average" ).trim() || "average"; const pregroupThreshold = finiteNumber( clusterSettings?.pregroupThreshold, 0.75, 0, 1 ); const pregroupLinkage = String( clusterSettings?.pregroupLinkage ?? "complete" ).trim() || "complete"; // ---------------------------------------------------------- // Subclustering // ---------------------------------------------------------- const minimumClusterSize = positiveInteger( subclusterSettings?.minimumClusterSize ?? subclusterSettings?.kMin, 6 ); const subclusterThreshold = finiteNumber( subclusterSettings?.subclusterThreshold ?? subclusterSettings?.subThreshold, 0.6, 0, 1 ); const subclusterLinkage = String( subclusterSettings?.subclusterLinkage ?? subclusterSettings?.subLinkage ?? "single" ).trim() || "single"; const performSubclustering = subclusterSettings?.performSubclustering ?? basicSettings?.performSubclustering ?? true; // ---------------------------------------------------------- // Heatmap settings // ---------------------------------------------------------- const gradientMode = String( heatmapSettings?.gradientMode ?? "Three-color gradient" ).trim(); const lowColor = String( heatmapSettings?.lowColor ?? "red" ).trim() || "red"; const middleColor = String( heatmapSettings?.middleColor ?? "" ).trim(); const highColor = String( heatmapSettings?.highColor ?? "green" ).trim() || "green"; /* <-- INSERT IT HERE */ if (heatmapSettings?.colorsValid === false) { throw new Error( "One or more heatmap colors are not supported CSS named colors." ); } const heatmapColors = gradientMode === "Two-color gradient" ? [ lowColor, highColor ].join(",") : [ lowColor, middleColor, highColor ].join(","); const heatmapMidpoint = finiteNumber( heatmapSettings?.heatmapMidpoint, 0.5, 0, 1 ); // ---------------------------------------------------------- // Run options // ---------------------------------------------------------- const debug = Boolean( runInformation?.debug ?? basicSettings?.debug ?? false ); const removeTemporaryFiles = Boolean( runInformation?.removeTemporaryFiles ?? runInformation?.removeTmp ?? false ); const commandArguments = [ ` "$INPUT_PATH"`, ` "$OUTPUT_DIR"`, ` --metric ${shQuote(metric)}`, ` --threads ${threads}`, ` --clu-thresh ${clusterThreshold}`, ` --clu-linkage ${shQuote(clusterLinkage)}`, ` --nr-thresh ${pregroupThreshold}`, ` --nr-linkage ${shQuote(pregroupLinkage)}`, ` --k-min ${minimumClusterSize}`, ` --sub-thresh ${subclusterThreshold}`, ` --sub-linkage ${shQuote(subclusterLinkage)}`, ` --heatmap-colors ${shQuote(heatmapColors)}`, ` --heatmap-midpoint ${heatmapMidpoint}` ]; if (!performSubclustering) { commandArguments.push( " --no-sub" ); } if (removeTemporaryFiles) { commandArguments.push( " --remove-tmp" ); } if (debug) { commandArguments.push( " --debug" ); } const phamclustCommand = "phamclust \\\n" + commandArguments.join(" \\\n"); return `bash <<'PHAMCLUST_SCRIPT' #!/usr/bin/env bash set -Eeuo pipefail trap 'status=$?; echo; echo "❌ PhamClust failed at line $LINENO (exit $status)"; exit $status' ERR # ============================================================ # PhamClust analysis # Generated by the Observable PhamClust notebook # ============================================================ ENV_NAME=${shQuote(environmentName)} INPUT_PATH=${shQuote(inputPath)} OUTPUT_DIR=${shQuote(outputDirectory)} # ------------------------------------------------------------ # Locate Conda # ------------------------------------------------------------ if command -v conda >/dev/null 2>&1; then CONDA_BASE="$(conda info --base)" elif [ -f "$HOME/miniconda/bin/conda" ]; then CONDA_BASE="$HOME/miniconda" elif [ -f "$HOME/miniconda3/bin/conda" ]; then CONDA_BASE="$HOME/miniconda3" elif [ -f "$HOME/miniforge3/bin/conda" ]; then CONDA_BASE="$HOME/miniforge3" else echo "❌ Conda was not found in WSL." >&2 exit 1 fi if [ ! -f "$CONDA_BASE/etc/profile.d/conda.sh" ]; then echo "❌ Conda initialization file was not found:" >&2 echo " $CONDA_BASE/etc/profile.d/conda.sh" >&2 exit 1 fi source "$CONDA_BASE/etc/profile.d/conda.sh" # ------------------------------------------------------------ # Confirm that the environment exists # ------------------------------------------------------------ if ! conda env list | awk '{print $1}' | grep -Fxq "$ENV_NAME"; then echo "❌ Conda environment '$ENV_NAME' does not exist." >&2 echo "Run the PhamClust installer first." >&2 exit 1 fi conda activate "$ENV_NAME" # ------------------------------------------------------------ # Confirm that PhamClust is installed # ------------------------------------------------------------ if ! command -v phamclust >/dev/null 2>&1; then echo "❌ phamclust was not found in environment '$ENV_NAME'." >&2 exit 1 fi # ------------------------------------------------------------ # Validate paths # ------------------------------------------------------------ if [ -z "$INPUT_PATH" ]; then echo "❌ No input TSV path was provided." >&2 exit 1 fi if [ ! -f "$INPUT_PATH" ]; then echo "❌ Input TSV file was not found:" >&2 echo " $INPUT_PATH" >&2 exit 1 fi if [ -z "$OUTPUT_DIR" ]; then echo "❌ No output directory was provided." >&2 exit 1 fi mkdir -p "$OUTPUT_DIR" # ------------------------------------------------------------ # Run summary # ------------------------------------------------------------ echo "============================================================" echo " Starting PhamClust" echo "============================================================" echo "Conda base: $CONDA_BASE" echo "Conda environment: $ENV_NAME" echo "Input TSV: $INPUT_PATH" echo "Output directory: $OUTPUT_DIR" echo "Metric: ${metric}" echo "CPU cores: ${threads}" echo "Main threshold: ${clusterThreshold}" echo "Main linkage: ${clusterLinkage}" echo "Pre-group threshold: ${pregroupThreshold}" echo "Pre-group linkage: ${pregroupLinkage}" echo "Minimum cluster size: ${minimumClusterSize}" echo "Subcluster threshold: ${subclusterThreshold}" echo "Subcluster linkage: ${subclusterLinkage}" echo "Heatmap colors: ${heatmapColors}" echo "Heatmap midpoint: ${heatmapMidpoint}" echo "Subclustering enabled: ${ performSubclustering ? "yes" : "no" }" echo "Remove temporary files: ${ removeTemporaryFiles ? "yes" : "no" }" echo "Debug mode: ${ debug ? "yes" : "no" }" echo # ------------------------------------------------------------ # Run PhamClust # ------------------------------------------------------------ ${phamclustCommand} echo echo "============================================================" echo "✅ PhamClust completed successfully." echo "============================================================" echo echo "Results were written to:" echo " $OUTPUT_DIR" PHAMCLUST_SCRIPT`; }37:T664,//Complete normalizedPhages = (phameratorGenomes ?? []) .map((d) => { const cluster = String(d.cluster ?? "").trim(); const subclusterRaw = String(d.subcluster ?? "").trim(); /* * Some datasets store subcluster as only the suffix ("1"), * while others may use the combined value ("A1"). */ const clusterSubcluster = String( d.clusterSubcluster ?? (cluster && subclusterRaw ? `${cluster}${subclusterRaw}` : cluster) ).trim(); return { ...d, phage_name: String( d.phagename ?? d.phage_name ?? d.name ?? "" ).trim(), cluster, subcluster: subclusterRaw ? ( cluster && !subclusterRaw.startsWith(cluster) ? `${cluster}${subclusterRaw}` : subclusterRaw ) : "", cluster_subcluster: clusterSubcluster, genome_length: Number(d.genomelength ?? d.genome_length ?? 0) || null, dataset: String(d.dataset ?? dataset ?? "").trim(), /* * These optional fields are retained if a private dataset * includes them. The normal /genomes endpoint may leave them blank. */ host_genus: String(d.host_genus ?? d.genus ?? "").trim(), host_species: String(d.host_species ?? d.species ?? "").trim(), host_strain: String(d.host_strain ?? d.strain ?? "").trim(), institution_name: String( d.institution_name ?? d.institution ?? "" ).trim() }; }) .filter((d) => d.phage_name) .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)) 38:T52d,fetchSelectedPhageGenes = async ( phageNames, concurrency = 6 ) => { const names = [...new Set( (phageNames ?? []) .map((name) => String(name).trim()) .filter(Boolean) )]; const results = new Array(names.length); const errors = []; let nextIndex = 0; async function worker() { while (true) { const index = nextIndex++; if (index >= names.length) return; const phageName = names[index]; try { const genes = await phameratorGet( `/genes/${encodeURIComponent(phageName)}` ); if (!Array.isArray(genes)) { throw new Error( "The endpoint did not return an array." ); } results[index] = { phageName, genes }; } catch (error) { results[index] = { phageName, genes: [] }; errors.push({ phageName, message: error?.message ?? String(error) }); } } } const workerCount = Math.max( 1, Math.min( Number(concurrency) || 1, names.length || 1 ) ); await Promise.all( Array.from( { length: workerCount }, () => worker() ) ); return { requestedPhages: names, results, errors }; } 39:T41c,selectedGeneRecords = { const groups = selectedGeneFetch?.results ?? []; return groups.flatMap(({ phageName, genes }) => (genes ?? []).map((gene) => ({ phage_name: String( gene.phageID ?? gene.phagename ?? gene.phage_name ?? phageName ?? "" ) .trim() .replace(/_Draft$/i, ""), gene_name: String(gene.name ?? gene.gene_name ?? "").trim(), gene_id: String(gene.geneID ?? gene.GeneID ?? gene.gene_id ?? "").trim(), locus_tag: String(gene.LocusTag ?? gene.locus_tag ?? "").trim(), pham: String( gene.phamName ?? gene.PhamID ?? gene.pham ?? gene.pham_id ?? "" ).trim(), translation: String( gene.translation ?? gene.protein_translation ?? gene.amino_acid_sequence ?? "" ) .replace(/\s+/g, "") .trim(), function: String(gene.genefunction ?? gene.function ?? "").trim(), start: Number(gene.start ?? gene.Start) || null, stop: Number(gene.stop ?? gene.Stop) || null })) ); } 3a:T700,phamclustValidation = { const source = selectedGeneRecords ?? []; const valid = phamclustRows ?? []; const requestedPhages = (selectedGeneFetch?.requestedPhages ?? []) .map((name) => String(name ?? "") .trim() .replace(/_Draft$/i, "") ) .filter(Boolean); const returnedPhages = new Set( source .map((d) => d.phage_name) .filter(Boolean) ); const phagesWithNoGenes = requestedPhages.filter((name) => !returnedPhages.has(name) ); const missingPhage = source.filter( (d) => !d.phage_name ); const missingPham = source.filter( (d) => !d.pham ); const missingTranslation = source.filter( (d) => !d.translation ); const invalidTranslation = source.filter( (d) => d.translation && !isValidProteinTranslation(d.translation) ); const duplicateKeys = new Map(); for (const row of valid) { const key = [ row.phage_name, row.pham, row.translation ].join("\t"); duplicateKeys.set( key, (duplicateKeys.get(key) ?? 0) + 1 ); } const exactDuplicateRows = [...duplicateKeys.values()] .filter((count) => count > 1) .reduce( (sum, count) => sum + count - 1, 0 ); return { requestedPhages: requestedPhages.length, returnedPhages: returnedPhages.size, sourceGenes: source.length, exportableGenes: valid.length, uniquePhams: new Set( valid.map((d) => d.pham) ).size, missingPhage: missingPhage.length, missingPham: missingPham.length, missingTranslation: missingTranslation.length, invalidTranslation: invalidTranslation.length, exactDuplicateRows, phagesWithNoGenes, requestErrors: selectedGeneFetch?.errors ?? [] }; } 3b:[] 2c:{"id":"1f3b8f465e71d5b3","slug":"phamclust","title":"PEQ Heatmap using PhamClust","thumbnail":"1e33e1d533dfb5bda5e7767a1bc2dd6a3ce89e26450af9e3ab7032fee8f710e0","access_level":"public","create_time":"$D2026-07-13T15:06:32.009Z","update_time":"$D2026-08-05T20:47:19.444Z","view_time":null,"first_public_time":"$D2026-07-31T17:15:52.493Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"d1dfc5f860fb8699","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":"starter_2024"},"version":551,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"3035ce62f81ebcd9","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":null}],"members":[{"type":"individual","id":"3035ce62f81ebcd9","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":null,"role":"editor"},{"type":"team","id":"d1dfc5f860fb8699","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":true,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"PEQ Heatmap using PhamClust","cells":[{"id":437,"value":"# PEQ Heatmap using PhamClust\n\nThis notebook provides:\n\n- Code to install:\n - Windows Subsystem for Linux (WSL) (required to run PhamClust code)
\n - PhamClust \n- Script to generate a .TSV file of Phages, Phams, and Genes for PhamClust\n- Script to generate WSL code to run PhamClust\n- A figure legend for the PhamClust heatmap\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":446,"value":"---","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":485,"value":"## Generate code to run PhamClust\n\n1. Enter PhamClust settings and copy generated WSL code\n2. Launch WSL and run copied WSL code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":112,"value":"$2e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":514,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":211,"value":"---","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":464,"value":"## Generate .TSV of Phages, Phams, & Genes\n\n1. Log into Phamerator with an API key\n2. Select phages and retrieve gene data\n3. Download .TSV file\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":167,"value":"viewof apiKey = {\n const storageKey = \"phamerator_api_key\";\n const savedKey = localStorage.getItem(storageKey) ?? \"\";\n\n const input = Inputs.password({\n label: \"🔑 Phamerator API key\",\n value: savedKey,\n placeholder: \"Enter your Phamerator API key\",\n style: \"width:420px\"\n });\n\n input.addEventListener(\"input\", () => {\n const key = input.value.trim();\n\n if (key) {\n localStorage.setItem(storageKey, key);\n } else {\n localStorage.removeItem(storageKey);\n }\n });\n\n return input;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":184,"value":"viewof dataset = Inputs.select(availableDatasets, {\n label: \"🗃️ Phamerator dataset\",\n value: availableDatasets.includes(\"Actino_Draft\")\n ? \"Actino_Draft\"\n : availableDatasets[0],\n disabled: availableDatasets.length === 0\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":340,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":274,"value":"viewof geneLoadRequest = Inputs.button(\n \"🧬 Retrieve genes for selected phages\",\n {\n disabled: !resultsTable?.selectedPhageNames?.length,\n\n reduce: () => ({\n requestedAt: Date.now(),\n dataset,\n phageNames: [...(resultsTable?.selectedPhageNames ?? [])].sort(\n d3.ascending\n )\n })\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":288,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":391,"value":"excludedGeneRecords.length\n ? Inputs.table(excludedGeneRecords, {\n columns: [\n \"phage\",\n \"gene\",\n \"geneID\",\n \"pham\",\n \"translationLength\",\n \"reason\"\n ],\n header: {\n phage: \"Phage\",\n gene: \"Gene\",\n geneID: \"Gene ID\",\n pham: \"Pham\",\n translationLength: \"Translation length\",\n reason: \"Reason excluded\"\n },\n rows: 20\n })\n : html`\n

\n ✅ No gene records were excluded.\n

\n `","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":292,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":296,"value":"{\n const selectedCount = geneLoadRequest?.phageNames?.length ?? 0;\n\n const safeDataset = String(dataset ?? \"dataset\").replace(\n /[^A-Za-z0-9._-]+/g,\n \"_\"\n );\n\n const fileName = `${safeDataset}_phamclust_` + `${selectedCount}_phages.tsv`;\n\n return phamclustTSV\n ? DOM.download(\n new Blob([phamclustTSV + \"\\n\"], {\n type: \"text/tab-separated-values;charset=utf-8\"\n }),\n fileName,\n `⬇ Download ${fileName}`\n )\n : html`\n \n `;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":140,"value":"---\n## Install WSL and PhamClust","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":508,"value":"WSL is used to run code that runs PhamClust","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":144,"value":"viewof wslInstallGuide = {\n const container = html`

Install WSL on Windows

To run Dorado and other Linux-based tools on Windows, you’ll first need to install WSL (Windows Subsystem for Linux).

\n\n

Install WSL
\n Windows Start Menu, find & run PowerShell as Administrator, then run the following code:\n
```
wsl --install
```
\n Then restart your computer.\n
Install a Linux Distribution (e.g., Ubuntu)
\n After restarting, run WSL from the Start menu:
\n \n

`;\n\n return container;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":90,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":55,"value":"---\n## Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":12,"value":"windowsToWSLPath = (path) => {\n const value = String(path ?? \"\").trim();\n\n if (!value) return \"\";\n\n // Leave paths that are already in Linux/WSL format unchanged.\n if (value.startsWith(\"/\")) {\n return value;\n }\n\n // Convert C:\\Folder\\File or C:/Folder/File to /mnt/c/Folder/File.\n const match = value.match(/^([A-Za-z]):[\\\\/](.*)$/);\n\n if (!match) {\n return value.replace(/\\\\/g, \"/\");\n }\n\n const drive = match[1].toLowerCase();\n const remainder = match[2].replace(/\\\\/g, \"/\");\n\n return `/mnt/${drive}/${remainder}`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10,"value":"shellQuote = value => {\n const text = String(value ?? \"\");\n return `'${text.replaceAll(\"'\", `'\\\\''`)}'`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":16,"value":"resolvedPaths = {\n const convert =\n pathSettings.pathStyle === \"Windows paths — convert automatically to WSL\";\n return {\n input: convert\n ? windowsToWSLPath(pathSettings.inputPath)\n : String(pathSettings.inputPath ?? \"\").trim(),\n output: convert\n ? windowsToWSLPath(pathSettings.outputDirectory)\n : String(pathSettings.outputDirectory ?? \"\").trim()\n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":24,"value":"viewof pathSettings = Inputs.form(\n {\n pathStyle: Inputs.select(\n [\"WSL/Linux paths\", \"Windows paths — convert automatically to WSL\"],\n {\n label: \"Path format entered below\",\n value: \"Windows paths — convert automatically to WSL\"\n }\n ),\n\n inputPath: Inputs.text({\n label: \"PhamClust input TSV file\",\n value: \"\",\n placeholder: \"C:\\\\Users\\\\kiera\\\\Downloads\\\\AZ_genes_reduced_tsv.tsv\",\n style: \"width:100%;\"\n }),\n\n outputDirectory: Inputs.text({\n label: \"PhamClust output directory\",\n value: \"\",\n placeholder: \"C:\\\\Users\\\\kiera\\\\Downloads\\\\PhamClust_AZ\",\n style: \"width:100%;\"\n })\n },\n {\n label: \"Input and output paths\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":26,"value":"viewof basicSettings = Inputs.form(\n {\n metric: Inputs.select([\"peq\", \"gcs\", \"jc\", \"pocp\", \"af\", \"aai\"], {\n label: \"Genome similarity metric\",\n value: \"peq\"\n }),\n\n threads: Inputs.range([1, 64], {\n label: \"CPU cores\",\n value: 8,\n step: 1\n }),\n\n performSubclustering: Inputs.toggle({\n label: \"Perform subclustering\",\n value: true\n }),\n\n removeTemporaryFiles: Inputs.toggle({\n label: \"Remove temporary files after the run\",\n value: false\n }),\n\n debugLogging: Inputs.toggle({\n label: \"Enable detailed debug logging\",\n value: false\n })\n },\n {\n label: \"Basic analysis settings\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"viewof clusterSettings = Inputs.form(\n {\n clusterThreshold: Inputs.number({\n label: \"Main clustering similarity threshold\",\n value: 0.25,\n min: 0,\n max: 1,\n step: 0.01\n }),\n\n clusterLinkage: Inputs.select(\n [\n \"average\",\n \"single\",\n \"complete\"\n ],\n {\n label: \"Main clustering linkage\",\n value: \"average\"\n }\n ),\n\n pregroupThreshold: Inputs.number({\n label: \"Highly similar genome pre-grouping threshold\",\n value: 0.75,\n min: 0,\n max: 1,\n step: 0.01\n }),\n\n pregroupLinkage: Inputs.select(\n [\n \"complete\",\n \"average\",\n \"single\"\n ],\n {\n label: \"Pre-grouping linkage\",\n value: \"complete\"\n }\n )\n },\n {\n label: \"Main clustering settings\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":32,"value":"viewof subclusterSettings = Inputs.form(\n {\n minimumClusterSize: Inputs.range([2, 50], {\n label: \"Minimum cluster size for subclustering\",\n value: 6,\n step: 1\n }),\n\n subclusterThreshold: Inputs.range([0, 1], {\n label: \"Subclustering similarity threshold\",\n value: 0.6,\n step: 0.01\n }),\n\n subclusterLinkage: Inputs.select([\"single\", \"average\", \"complete\"], {\n label: \"Subclustering linkage\",\n value: \"single\"\n })\n },\n {\n label: \"Subclustering\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":71,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":74,"value":"viewof runInformation = Inputs.form(\n {\n analysisName: Inputs.text({\n label: \"Analysis name\",\n value: \"PhamClust analysis\",\n placeholder: \"PhamClust analysis\"\n }),\n\n notes: Inputs.textarea({\n label: \"Notes added to the generated script\",\n value: \"\",\n placeholder: \"Optional description of this analysis\",\n rows: 3\n })\n },\n {\n label: \"Run information\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":106,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":110,"value":"$36","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":102,"value":"html`\n

\n Resolved input:
\n ${resolvedPaths.input || \"No input path entered\"}\n

\n\n

\n Resolved output:
\n ${resolvedPaths.output || \"No output path entered\"}\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":169,"value":"## Phamerator Log-In Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":213,"value":"import {\n getPhameratorData,\n terms,\n styles\n} from \"@scresawn/phamerator-api-utilities\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":172,"value":"getPhameratorUser = async (apiKey) => {\n const key = String(apiKey ?? \"\").trim();\n\n if (!key) {\n return null;\n }\n\n const response = await fetch(\"https://classic.phamerator.org/api/profile\", {\n headers: {\n Authorization: `Bearer ${key}`,\n Accept: \"application/json\"\n }\n });\n\n if (!response.ok) {\n let detail = \"\";\n\n try {\n const body = await response.text();\n detail = body ? `: ${body}` : \"\";\n } catch {\n // Ignore failure to read error body.\n }\n\n throw new Error(\n `Phamerator login failed (${response.status} ${response.statusText})${detail}`\n );\n }\n\n const profile = await response.json();\n\n // Avoid retaining API-key metadata from the server response.\n if (profile && typeof profile === \"object\") {\n delete profile.apiKeys;\n }\n\n return profile;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":175,"value":"user = {\n const key = String(apiKey ?? \"\").trim();\n\n if (!key) return null;\n\n const response = await fetch(\"https://classic.phamerator.org/api/profile\", {\n headers: {\n Authorization: `Bearer ${key}`,\n Accept: \"application/json\"\n }\n });\n\n if (!response.ok) {\n throw new Error(\n `Phamerator login failed: ${response.status} ${response.statusText}`\n );\n }\n\n const profile = await response.json();\n\n // Do not retain or display API-key metadata returned by the server.\n if (profile && typeof profile === \"object\") {\n delete profile.apiKeys;\n }\n\n return profile;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":222,"value":"availableDatasets = Array.isArray(user?.datasets)\n ? [...user.datasets].sort(d3.ascending)\n : []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":225,"value":"//Complete\nphameratorGet = async (endpoint) => {\n if (!user) {\n throw new Error(\"Enter a valid Phamerator API key first.\");\n }\n\n if (!dataset) {\n throw new Error(\"Select a Phamerator dataset first.\");\n }\n\n /*\n * The Phamerator utility accepts:\n * dataset, endpoint, email, password/API key\n *\n * The profile request supplies the authenticated email.\n * The API key is passed as the credential.\n */\n return await getPhameratorData(\n dataset,\n endpoint,\n user.email,\n String(apiKey).trim()\n );\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":321,"value":"## Get Phamerator Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":228,"value":"//Complete\nphameratorGenomes = {\n if (!user || !dataset) return [];\n\n const data = await phameratorGet(\"/genomes\");\n\n if (!Array.isArray(data)) {\n throw new Error(\n \"The Phamerator /genomes endpoint did not return an array.\"\n );\n }\n\n return data;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":231,"value":"$37","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":234,"value":"//Complete\nphageDatasetSummary = {\n const rows = normalizedPhages ?? [];\n\n return {\n dataset,\n phages: rows.length,\n clusters: new Set(rows.map((d) => d.cluster).filter(Boolean)).size,\n subclusters: new Set(rows.map((d) => d.subcluster).filter(Boolean)).size\n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":360,"value":"//Complete\navailablePhageRows = normalizedPhages ?? []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":276,"value":"$38","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":278,"value":"selectedGeneFetch = {\n if (!geneLoadRequest?.requestedAt) {\n return {\n requestedPhages: [],\n results: [],\n errors: []\n };\n }\n\n return await fetchSelectedPhageGenes(\n geneLoadRequest.phageNames,\n 6\n );\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":280,"value":"$39","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":282,"value":"isValidProteinTranslation = (sequence) => {\n const value = String(sequence ?? \"\")\n .replace(/\\s+/g, \"\")\n .toUpperCase();\n\n /*\n * Standard amino-acid symbols plus:\n * B = Asn/Asp ambiguity\n * Z = Gln/Glu ambiguity\n * J = Leu/Ile ambiguity\n * X = unknown\n * U = selenocysteine\n * O = pyrrolysine\n * * = terminal stop, tolerated then removed for export\n */\n return Boolean(value) &&\n /^[ABCDEFGHIKLMNPQRSTVWXYZUO*]+$/.test(value);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":284,"value":"phamclustRows = {\n return (selectedGeneRecords ?? [])\n .map((d) => ({\n ...d,\n\n translation: String(d.translation ?? \"\")\n .replace(/\\s+/g, \"\")\n .replace(/\\*+$/g, \"\")\n .toUpperCase()\n }))\n .filter(\n (d) =>\n d.phage_name &&\n d.pham &&\n d.translation &&\n isValidProteinTranslation(d.translation)\n )\n .sort((a, b) =>\n d3.ascending(a.phage_name, b.phage_name) ||\n d3.ascending(\n Number(a.gene_name) || a.gene_name,\n Number(b.gene_name) || b.gene_name\n )\n );\n}\n\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":286,"value":"$3a","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":298,"value":"excludedGeneRecords = {\n const validObjects = new Set(phamclustRows);\n\n return (selectedGeneRecords ?? [])\n .filter((d) => {\n const normalized = {\n ...d,\n\n translation: String(d.translation ?? \"\")\n .replace(/\\s+/g, \"\")\n .replace(/\\*+$/g, \"\")\n .toUpperCase()\n };\n\n return !(\n normalized.phage_name &&\n normalized.pham &&\n normalized.translation &&\n isValidProteinTranslation(normalized.translation)\n );\n })\n .map((d) => ({\n phage: d.phage_name,\n gene: d.gene_name,\n geneID: d.gene_id,\n pham: d.pham,\n translationLength: d.translation?.length ?? 0,\n\n reason: !d.phage_name\n ? \"Missing phage name\"\n : !d.pham\n ? \"Missing pham\"\n : !d.translation\n ? \"Missing translation\"\n : \"Invalid amino-acid characters\"\n }));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":290,"value":"phamclustTSV = (phamclustRows ?? [])\n .map((d) => [d.phage_name, d.pham, d.translation].join(\"\\t\"))\n .join(\"\\n\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":362,"value":"---","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"}],"files":"$W3b","stdlib":"1","titling":"auto"}} 2d:"$2c:body"