28:null 29:["$","title",null,{"children":"Clusters by Host Genus, Species, & Strain | WabushOnce | Observable"}] 2e:T1fd7,controls = { const getGenus = (d) => d.genus ?? d.host_genus ?? ""; const getSpecies = (d) => d.species ?? d.host_species ?? ""; const getStrain = (d) => d.strain ?? d.host_strain ?? ""; const genusOptions = [ ...new Set(normalizedPhages.map(getGenus).filter(Boolean)) ].sort(d3.ascending); const speciesOptions = selectedGenera.length ? [ ...new Set( normalizedPhages .filter((d) => selectedGenera.includes(getGenus(d))) .map(getSpecies) .filter(Boolean) ) ].sort(d3.ascending) : [...new Set(normalizedPhages.map(getSpecies).filter(Boolean))].sort( d3.ascending ); const strainOptions = selectedSpeciesList.length ? [ ...new Set( normalizedPhages .filter((d) => selectedSpeciesList.includes(getSpecies(d))) .map(getStrain) .filter(Boolean) ) ].sort(d3.ascending) : selectedGenera.length ? [ ...new Set( normalizedPhages .filter((d) => selectedGenera.includes(getGenus(d))) .map(getStrain) .filter(Boolean) ) ].sort(d3.ascending) : [...new Set(normalizedPhages.map(getStrain).filter(Boolean))].sort( d3.ascending ); const wrap = html`

`; const left = wrap.querySelector(".left"); const right = wrap.querySelector(".right"); const buttonStyle = ` padding:6px 12px; border:1px solid #ccc; border-radius:8px; background:white; cursor:pointer; font:13px sans-serif; `; const selectStyle = ` padding:6px 10px; border:1px solid #ccc; border-radius:8px; background:white; font:13px sans-serif; min-width:240px; min-height:120px; `; const backBtn = html``; const resetBtn = html``; const genusBox = html`

Host genus (one or more)

`; const speciesBox = html`

Host species (one or more)

`; const strainBox = html`

Host strain (one or more)

`; const genusSelect = genusBox.querySelector("select"); const speciesSelect = speciesBox.querySelector("select"); const strainSelect = strainBox.querySelector("select"); function fillMultiSelect(select, options, selectedValues) { select.innerHTML = ""; for (const value of options) { const option = html``; option.selected = selectedValues.includes(value); select.append(option); } } function selectedValues(select) { return [...select.selectedOptions].map((o) => o.value); } function syncControls() { fillMultiSelect(genusSelect, genusOptions, selectedGenera); const currentSpeciesOptions = selectedGenera.length ? [ ...new Set( normalizedPhages .filter((d) => selectedGenera.includes(getGenus(d))) .map(getSpecies) .filter(Boolean) ) ].sort(d3.ascending) : [...new Set(normalizedPhages.map(getSpecies).filter(Boolean))].sort( d3.ascending ); fillMultiSelect( speciesSelect, currentSpeciesOptions, selectedSpeciesList.filter((v) => currentSpeciesOptions.includes(v)) ); const currentStrainOptions = selectedSpeciesList.length ? [ ...new Set( normalizedPhages .filter((d) => selectedSpeciesList.includes(getSpecies(d))) .map(getStrain) .filter(Boolean) ) ].sort(d3.ascending) : selectedGenera.length ? [ ...new Set( normalizedPhages .filter((d) => selectedGenera.includes(getGenus(d))) .map(getStrain) .filter(Boolean) ) ].sort(d3.ascending) : [...new Set(normalizedPhages.map(getStrain).filter(Boolean))].sort( d3.ascending ); fillMultiSelect( strainSelect, currentStrainOptions, selectedStrainsList.filter((v) => currentStrainOptions.includes(v)) ); } [backBtn, resetBtn].forEach((btn) => { btn.onmouseenter = () => (btn.style.background = "#f5f5f5"); btn.onmouseleave = () => (btn.style.background = "white"); }); genusSelect.onchange = () => { const genera = selectedValues(genusSelect); mutable selectedGenera = genera; const allowedSpecies = genera.length ? new Set( normalizedPhages .filter((d) => genera.includes(getGenus(d))) .map(getSpecies) .filter(Boolean) ) : null; const nextSpecies = genera.length ? selectedSpeciesList.filter((v) => allowedSpecies.has(v)) : selectedSpeciesList; mutable selectedSpeciesList = nextSpecies; const allowedStrains = nextSpecies.length ? new Set( normalizedPhages .filter((d) => nextSpecies.includes(getSpecies(d))) .map(getStrain) .filter(Boolean) ) : genera.length ? new Set( normalizedPhages .filter((d) => genera.includes(getGenus(d))) .map(getStrain) .filter(Boolean) ) : null; const nextStrains = allowedStrains ? selectedStrainsList.filter((v) => allowedStrains.has(v)) : selectedStrainsList; mutable selectedStrainsList = nextStrains; syncControls(); }; speciesSelect.onchange = () => { const species = selectedValues(speciesSelect); mutable selectedSpeciesList = species; const allowedStrains = species.length ? new Set( normalizedPhages .filter((d) => species.includes(getSpecies(d))) .map(getStrain) .filter(Boolean) ) : selectedGenera.length ? new Set( normalizedPhages .filter((d) => selectedGenera.includes(getGenus(d))) .map(getStrain) .filter(Boolean) ) : null; const nextStrains = allowedStrains ? selectedStrainsList.filter((v) => allowedStrains.has(v)) : selectedStrainsList; mutable selectedStrainsList = nextStrains; syncControls(); }; strainSelect.onchange = () => { mutable selectedStrainsList = selectedValues(strainSelect); syncControls(); }; backBtn.onclick = () => { if (selectedStrainsList.length) { mutable selectedStrainsList = []; } else if (selectedSpeciesList.length) { mutable selectedSpeciesList = []; } else if (selectedGenera.length) { mutable selectedGenera = []; } syncControls(); }; resetBtn.onclick = () => { mutable selectedGenera = []; mutable selectedSpeciesList = []; mutable selectedStrainsList = []; syncControls(); }; left.append(genusBox, speciesBox, strainBox); right.append(backBtn, resetBtn); syncControls(); return wrap; }2f:T277c,display = { const totalPhages = phages.length; const totalClusters = new Set(phages.map((d) => d.cluster).filter(Boolean)) .size; const totalSubclusters = new Set( phages.map((d) => d.subcluster).filter(Boolean) ).size; const rows = selectedRows ?? []; const clusterToSubclusters = d3.rollup( rows.filter((d) => d.cluster), (v) => new Set(v.map((d) => d.subcluster).filter(Boolean)), (d) => d.cluster ); const clustersWithoutSubclusters = [...clusterToSubclusters.entries()] .filter(([, subSet]) => subSet.size === 0) .map(([cluster]) => cluster) .sort(d3.ascending); const clustersWithSubclusters = [...clusterToSubclusters.entries()] .filter(([, subSet]) => subSet.size > 0) .map(([cluster]) => cluster) .sort(d3.ascending); const subclusterNames = [ ...new Set(rows.map((d) => d.subcluster).filter(Boolean)) ].sort(d3.ascending); const phageNames = [ ...new Set(rows.map((d) => d.phage_name).filter(Boolean)) ].sort(d3.ascending); const pct = (value, total) => total > 0 ? `${((100 * value) / total).toFixed(1)}%` : "0.0%"; return html`

${ summary.selectedLabel }: ${summary.selectedValue}

Phages: ${summary.phages} / ${totalPhages} (${pct( summary.phages, totalPhages )})

Clusters: ${summary.clusters} / ${totalClusters} (${pct( summary.clusters, totalClusters )})

Subclusters: ${summary.subclusters} / ${totalSubclusters} (${pct( summary.subclusters, totalSubclusters )})

Clusters without subclusters in current selection (${ clustersWithoutSubclusters.length })

${ clustersWithoutSubclusters.length ? clustersWithoutSubclusters.map( (name) => html` ${name} ` ) : html`None` }

Clusters with subclusters in current selection (${ clustersWithSubclusters.length })

${ clustersWithSubclusters.length ? clustersWithSubclusters.map( (name) => html` ${name} ` ) : html`None` }

Subclusters in current selection (${subclusterNames.length})

${ subclusterNames.length ? subclusterNames.map( (name) => html` ${name} ` ) : html`None` }

${ level === "strainDetail" ? html`

Phages for selected strain (${phageNames.length})

${ phageNames.length ? phageNames.map( (name) => html` ${name} ` ) : html`No phages found` }

` : html`

Phages in current selection (${phageNames.length})

${ phageNames.length ? phageNames.map( (name) => html` ${name} ` ) : html`No phages found` }

` }

`; }30:Tad3,cacheStatus = { const wrap = html`

`; const buttonStyle = ` padding:6px 12px; border:1px solid #ccc; border-radius:8px; background:white; cursor:pointer; font:13px sans-serif; `; const updateBtn = html``; updateBtn.onmouseenter = () => (updateBtn.style.background = "#f5f5f5"); updateBtn.onmouseleave = () => (updateBtn.style.background = "white"); updateBtn.onclick = async () => { updateBtn.textContent = "Updating..."; updateBtn.disabled = true; try { const fresh = await fetchPhagesFromAPI(); const added = hasNewPhages(phages, fresh); const modified = hasModifiedPhages(phages, fresh); let result; if (phages.length === 0 || added || modified) { const payload = { updatedAt: new Date().toISOString(), phages: fresh }; localStorage.setItem(cacheKey, JSON.stringify(payload)); mutable phages = fresh; mutable cacheUpdatedAt = payload.updatedAt; result = { updated: true, added, modified, count: fresh.length, updatedAt: payload.updatedAt, error: false }; } else { result = { updated: false, added: false, modified: false, count: fresh.length, updatedAt: cacheUpdatedAt, error: false }; } mutable updateResult = result; } catch (err) { console.error(err); mutable updateResult = { updated: false, error: true }; } updateBtn.textContent = "Update from PhagesDB"; updateBtn.disabled = false; }; wrap.querySelector(".status").append(html`

Cached phages: ${phages.length}

Last cache update: ${cacheUpdatedAt ?? "Never"}

${ updateResult ? html`

Last check: ${ updateResult.updated ? `cache refreshed (${updateResult.count} phages)` : `no changes found (${updateResult.count} phages checked)` }

` : "" }

`); wrap.querySelector(".actions").append(updateBtn); return wrap; }31:T68e,viewof formData = { const form = html` `; return formWithSubmit(form); }32:T643,viewof dataset = { const hasLogin = !!(user && user.email); const datasets = hasLogin && Array.isArray(user.datasets) ? user.datasets.slice().sort() : []; const wrap = html`

Phamerator data set

`; const control = wrap.querySelector(".control"); const note = wrap.querySelector(".note"); if (!hasLogin) { control.append(html` `); note.textContent = "The dataset selector will become active after login."; wrap.value = "Actino_Draft"; return wrap; } const initialValue = datasets.includes("Actino_Draft") ? "Actino_Draft" : datasets[0]; const select = Inputs.select(datasets, {value: initialValue}); control.append(select); note.textContent = `Available datasets: ${datasets.length}`; wrap.value = select.value; select.addEventListener("input", () => { wrap.value = select.value; wrap.dispatchEvent(new CustomEvent("input")); }); return wrap; }33:T792,viewof downloadMode = { const rows = selectedRows ?? []; const allPhageCount = rows.length; const onePerClusterCount = d3.groups( rows, (d) => d.cluster || "Unknown" ).length; const onePerClusterSubclusterCount = d3 .groups( rows, (d) => d.cluster || "Unknown", (d) => d.subcluster && d.subcluster.trim() !== "" ? d.subcluster : "__NO_SUBCLUSTER__" ) .reduce((total, [, subgroups]) => total + subgroups.length, 0); const wrap = html` `; wrap.value = "all"; wrap.addEventListener("change", () => { const selected = wrap.querySelector('input[name="download-mode"]:checked')?.value ?? "all"; wrap.value = selected; wrap.dispatchEvent(new CustomEvent("input")); }); return wrap; }34:T594,viewof fastaHeaderMode = { const wrap = html` `; wrap.value = "cluster_subcluster_phage"; wrap.addEventListener("change", () => { const selected = wrap.querySelector('input[name="header-mode"]:checked')?.value ?? "cluster_subcluster_phage"; wrap.value = selected; wrap.dispatchEvent(new CustomEvent("input")); }); return wrap; }35:T2928,downloadFastas = { const wrap = html`

`; const top = wrap.querySelector(".top"); const summary = wrap.querySelector(".summary"); const missing = wrap.querySelector(".missing"); const progressWrap = wrap.querySelector(".progress-wrap"); const progressBar = wrap.querySelector(".progress-bar"); const progressText = wrap.querySelector(".progress-text"); const buttonStyle = ` padding:6px 12px; border:1px solid #ccc; border-radius:8px; background:white; cursor:pointer; font:13px sans-serif; `; const btn = html``; const status = html``; const hasLogin = !!(user && user.email && user.password); if (hasLogin) { btn.onmouseenter = () => (btn.style.background = "#f5f5f5"); btn.onmouseleave = () => (btn.style.background = "white"); } else { btn.disabled = true; btn.style.background = "#f3f3f3"; btn.style.color = "#888"; btn.style.cursor = "not-allowed"; } function clean(value) { return (value ?? "") .toString() .trim() .replace(/\s+/g, "_") .replace(/[^A-Za-z0-9._-]/g, "_"); } function wrapSequence(seq, width = 80) { const lines = []; for (let i = 0; i < seq.length; i += width) { lines.push(seq.slice(i, i + width)); } return lines.join("\n"); } function getGenus(d) { return d.genus ?? d.host_genus ?? ""; } function getSpecies(d) { return d.species ?? d.host_species ?? ""; } function getStrain(d) { return d.strain ?? d.host_strain ?? ""; } function uniqueOrMultiple(values, fallback) { const uniq = [...new Set(values.filter(Boolean))]; if (uniq.length === 1) return uniq[0]; if (uniq.length === 0) return fallback; return "multiple"; } function setProgress(current, total, label = "") { const pct = total > 0 ? (current / total) * 100 : 0; progressWrap.style.display = "block"; progressBar.style.width = `${pct}%`; progressText.textContent = label || `${current} of ${total}`; } function resetProgress() { progressWrap.style.display = "none"; progressBar.style.width = "0%"; progressText.textContent = ""; } function buildHeader(p) { const cluster = clean(p.cluster || "Unknown"); const subcluster = clean(p.subcluster || "None"); const phage = clean(p.phage_name); if (fastaHeaderMode === "phage") { return `>${phage}`; } if (fastaHeaderMode === "cluster_phage") { return `>${cluster}_${phage}`; } return `>${cluster}_${subcluster}_${phage}`; } async function getGenomeSequenceFromPhamerator(phageName) { const entry = { phage_requested: phageName, tried_names: [], success: false, sequence_length: 0, error: null }; const namesToTry = [phageName, phageName + "_Draft"]; for (const name of namesToTry) { entry.tried_names.push(name); try { const genome = await getPhameratorData( dataset, `/genome/${name}`, user.email, user.password ); const sequence = (genome.sequence ?? "") .toString() .replace(/\s+/g, "") .replace(/[^A-Za-z]/g, "") .toUpperCase() .trim(); entry.sequence_length = sequence.length; if (!sequence) { entry.error = "Sequence empty"; continue; } entry.success = true; mutable phameratorDebug = [...phameratorDebug, entry]; return sequence; } catch (err) { entry.error = err.message; } } mutable phameratorDebug = [...phameratorDebug, entry]; throw new Error(entry.error || "All name attempts failed"); } function pickPhages(rows) { const sorted = rows .slice() .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)); if (downloadMode === "all") { return sorted; } if (downloadMode === "cluster") { const grouped = d3.groups(sorted, (d) => d.cluster || "Unknown"); return grouped .map(([, phagesInGroup]) => phagesInGroup[0]) .filter(Boolean); } const grouped = d3.groups( sorted, (d) => d.cluster || "Unknown", (d) => d.subcluster && d.subcluster.trim() !== "" ? d.subcluster : "__NO_SUBCLUSTER__" ); const picked = []; for (const [, subgroups] of grouped) { for (const [, phagesInGroup] of subgroups) { const pick = phagesInGroup[0]; if (pick) picked.push(pick); } } return picked; } if (!hasLogin) { status.textContent = "Login to Phamerator to enable FASTA downloads."; top.append(btn, status); return wrap; } btn.onclick = async () => { btn.disabled = true; btn.textContent = "Preparing..."; status.textContent = ""; summary.textContent = ""; missing.innerHTML = ""; mutable phameratorDebug = []; resetProgress(); try { const rows = selectedRows ?? []; if (!rows.length) { status.textContent = "No phages in the current selection."; btn.textContent = "Download FASTAs"; btn.disabled = false; return; } const phagesToDownload = pickPhages(rows); if (!phagesToDownload.length) { status.textContent = "No phages matched the current download rule."; btn.textContent = "Download FASTAs"; btn.disabled = false; return; } const hostGenus = uniqueOrMultiple(rows.map(getGenus), "unknown_genus"); const hostSpecies = uniqueOrMultiple( rows.map(getSpecies), "unknown_species" ); const hostStrain = uniqueOrMultiple( rows.map(getStrain), "unknown_strain" ); const clusterCount = new Set(rows.map((d) => d.cluster).filter(Boolean)) .size; const subclusterCount = new Set( rows.map((d) => d.subcluster).filter(Boolean) ).size; btn.textContent = `Downloading ${phagesToDownload.length} phages...`; setProgress( 0, phagesToDownload.length, `Starting download of ${phagesToDownload.length} phages` ); const records = []; const failures = []; for (let i = 0; i < phagesToDownload.length; i++) { const p = phagesToDownload[i]; status.textContent = `Fetching ${i + 1}/${phagesToDownload.length}: ${ p.phage_name }`; setProgress( i, phagesToDownload.length, `Fetching ${i + 1} of ${phagesToDownload.length}: ${p.phage_name}` ); try { const seq = await getGenomeSequenceFromPhamerator(p.phage_name); records.push(`${buildHeader(p)}\n${wrapSequence(seq)}`); } catch (err) { failures.push({ phage: p.phage_name, error: err.message }); } } setProgress( phagesToDownload.length, phagesToDownload.length, `Finished processing ${phagesToDownload.length} phages` ); console.log("DEBUG phameratorDebug:", phameratorDebug); console.log("FAILURES:", failures); if (!records.length) { summary.textContent = `0 phages were added to the FASTA file. ${failures.length} phages could not be added.`; if (failures.length) { missing.innerHTML = `

Phages not added:

${failures .map((d) => d.phage) .join(", ")}

`; } status.textContent = "No sequences downloaded. Check debug panel."; btn.disabled = false; btn.textContent = "Download FASTAs"; return; } const modePart = downloadMode === "all" ? "all_phages" : downloadMode === "cluster" ? "one_per_cluster" : "one_per_cluster_or_subcluster"; const fileName = clean( `${hostGenus}_${hostSpecies}_${hostStrain}_${records.length}phages_${clusterCount}clusters_${subclusterCount}subclusters_${modePart}_${fastaHeaderMode}` ) + ".fasta"; const blob = new Blob([records.join("\n\n")], { type: "text/plain;charset=utf-8" }); const url = URL.createObjectURL(blob); const a = html``; document.body.appendChild(a); a.click(); a.remove(); URL.revokeObjectURL(url); summary.textContent = `${records.length} phages were added to the FASTA file. ${failures.length} phages could not be added.`; if (failures.length) { missing.innerHTML = `

Phages not added:

${failures .map((d) => d.phage) .join(", ")}

`; } else { missing.textContent = "All selected phages were added successfully."; } status.textContent = `Downloaded ${records.length} sequences.`; } catch (err) { console.error(err); status.textContent = `Error: ${err.message}`; } btn.disabled = false; btn.textContent = "Download FASTAs"; }; top.append(btn, status); return wrap; }36:Ta80,downloadPhageTable = { const wrap = html`

`; const buttonStyle = ` padding:6px 12px; border:1px solid #ccc; border-radius:8px; background:white; cursor:pointer; font:13px sans-serif; `; const btn = html``; const status = html``; function clean(value) { return (value ?? "") .toString() .trim() .replace(/\s+/g, "_") .replace(/[^A-Za-z0-9._-]/g, "_"); } function csvEscape(value) { const s = (value ?? "").toString(); return `"${s.replace(/"/g, '""')}"`; } function getGenus(d) { return d.genus ?? d.host_genus ?? ""; } function getSpecies(d) { return d.species ?? d.host_species ?? ""; } function getStrain(d) { return d.strain ?? d.host_strain ?? ""; } btn.onmouseenter = () => (btn.style.background = "#f5f5f5"); btn.onmouseleave = () => (btn.style.background = "white"); btn.onclick = () => { const rows = (selectedRows ?? []) .slice() .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)); if (!rows.length) { status.textContent = "No phages in the current selection."; return; } const hostGenus = [...new Set(rows.map(getGenus).filter(Boolean))].join("_or_") || "unknown_genus"; const hostSpecies = [...new Set(rows.map(getSpecies).filter(Boolean))].join("_or_") || "unknown_species"; const hostStrain = [...new Set(rows.map(getStrain).filter(Boolean))].join("_or_") || "unknown_strain"; const lines = [ ["phage", "cluster", "subcluster"].map(csvEscape).join(","), ...rows.map((d) => [ csvEscape(d.phage_name), csvEscape(d.cluster), csvEscape(d.subcluster || "") ].join(",") ) ]; const fileName = clean( `${hostGenus}_${hostSpecies}_${hostStrain}_${rows.length}phages_table` ) + ".csv"; const blob = new Blob([lines.join("\n")], { type: "text/csv;charset=utf-8" }); const url = URL.createObjectURL(blob); const a = html``; document.body.appendChild(a); a.click(); a.remove(); URL.revokeObjectURL(url); status.textContent = `Downloaded table with ${rows.length} phages.`; }; wrap.append(btn, status); return wrap; }37:T8a0,fetchPhagesFromAPI = async function () { const baseUrl = "https://phagesdb.org/api/sequenced_phages/"; const candidates = [2000, 1000, 500, 200]; async function detectPageSize() { for (const size of candidates) { const url = `${baseUrl}?page=1&page_size=${size}`; const res = await fetch(url); if (!res.ok) continue; const json = await res.json(); const results = json.results || []; const count = json.count ?? 0; if (results.length === size || count <= size) return size; if (results.length > 0) return results.length; } return 200; } async function fetchAllPages(url, acc = []) { const res = await fetch(url); if (!res.ok) throw new Error(`Failed to fetch ${url}: ${res.status}`); const json = await res.json(); acc.push(...(json.results || [])); return json.next ? fetchAllPages(json.next, acc) : acc; } const pageSize = await detectPageSize(); const startUrl = `${baseUrl}?page=1&page_size=${pageSize}`; const rows = await fetchAllPages(startUrl); return rows .map((p) => { const host_genus = p.host_genus?.genus_name ?? "Unknown genus"; const host_species = p.host_species ? `${p.host_species.genus} ${p.host_species.species_name}` : "Unknown species"; const host_strain = p.isolation_host?.strain_name ?? "Unknown strain"; return { phage_name: p.phage_name ?? "Unknown phage", institution: p.p_institution?.institution_code ?? "", institution_name: p.p_institution?.institution_name ?? "", cluster: p.pcluster?.cluster ?? "Unknown", subcluster: p.psubcluster?.subcluster ?? "", host_genus, host_species, host_strain, // keep old field names too so existing controls/chart still work genus: host_genus, species: host_species, strain: host_strain, date_modified: p.date_modified ?? null, genome_length: p.genome_length ?? null, morphotype: p.morphotype ?? "", temperate: p.pcluster?.temperate ?? null, fasta_file: p.fasta_file ?? null }; }) .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)); }38:T520,innerData = { const getGenus = (d) => d.genus ?? d.host_genus ?? ""; const getSpecies = (d) => d.species ?? d.host_species ?? ""; const getStrain = (d) => d.strain ?? d.host_strain ?? ""; if (level === "genus") { return [ ...d3.rollup( phages, (v) => v.length, (d) => getGenus(d) ) ] .map(([name, value]) => ({ name, value })) .filter((d) => d.name) .sort((a, b) => d3.descending(a.value, b.value)); } if (level === "species") { return [ ...d3.rollup( phages.filter((d) => getGenus(d) === selectedGenus), (v) => v.length, (d) => getSpecies(d) ) ] .map(([name, value]) => ({ name, value })) .filter((d) => d.name) .sort((a, b) => d3.descending(a.value, b.value)); } if (level === "strain") { return [ ...d3.rollup( phages.filter((d) => getSpecies(d) === selectedSpecies), (v) => v.length, (d) => getStrain(d) ) ] .map(([name, value]) => ({ name, value })) .filter((d) => d.name) .sort((a, b) => d3.descending(a.value, b.value)); } const rows = phages.filter((d) => getStrain(d) === selectedStrain); return [ { name: selectedStrain ?? "Selected strain", value: rows.length } ]; }39:T416,summary = { const rows = selectedRows ?? []; const clusters = [ ...new Set(rows.map((d) => d.cluster).filter(Boolean)) ].sort(d3.ascending); const subclusters = [ ...new Set(rows.map((d) => d.subcluster).filter(Boolean)) ].sort(d3.ascending); const phageNames = [ ...new Set(rows.map((d) => d.phage_name).filter(Boolean)) ].sort(d3.ascending); const selectedLabel = selectedStrainsList.length ? "Selected Strains" : selectedSpeciesList.length ? "Selected Species" : selectedGenera.length ? "Selected Genera" : "Selected Host Filter"; const selectedValue = selectedStrainsList.length ? selectedStrainsList.join(", ") : selectedSpeciesList.length ? selectedSpeciesList.join(", ") : selectedGenera.length ? selectedGenera.join(", ") : "All"; return { selectedLabel, selectedValue, phages: rows.length, clusters: clusters.length, subclusters: subclusters.length, phageNames, clusterNames: clusters, subclusterNames: subclusters }; }3a:T13db,makeChart = () => { const width = 840; const height = 840; const innerRadius0 = 105; const innerRadius1 = 210; const outerRadius0 = 235; const outerRadius1 = 365; const centerRadius = 92; const format = d3.format(","); const svg = d3 .create("svg") .attr("width", width) .attr("height", height) .attr("viewBox", [-width / 2, -height / 2, width, height]) .attr("preserveAspectRatio", "xMinYMin meet") .style("display", "block") .style("width", "100%") .style("max-width", `${width}px`) .style("height", "auto") .style("margin", "0") .style("background", "white") .style("font", "12px sans-serif"); const innerPie = d3 .pie() .sort(null) .value((d) => d.value); const outerPie = d3 .pie() .sort(null) .value((d) => d.value); const innerArc = d3.arc().innerRadius(innerRadius0).outerRadius(innerRadius1); const outerArc = d3.arc().innerRadius(outerRadius0).outerRadius(outerRadius1); const innerLabelArc = d3 .arc() .innerRadius((innerRadius0 + innerRadius1) / 2) .outerRadius((innerRadius0 + innerRadius1) / 2); const outerLabelArc = d3 .arc() .innerRadius((outerRadius0 + outerRadius1) / 2) .outerRadius((outerRadius0 + outerRadius1) / 2); const innerArcs = innerPie(innerData); const outerArcs = outerPie(outerData); const innerColor = d3.scaleOrdinal( d3.quantize(d3.interpolateSpectral, Math.max(3, innerData.length + 1)) ); const outerColor = d3.scaleOrdinal( d3.quantize(d3.interpolateRainbow, Math.max(3, outerData.length + 1)) ); svg .append("g") .selectAll("path") .data(outerArcs) .join("path") .attr("d", outerArc) .attr("fill", (d) => outerColor(d.data.name)) .attr("stroke", "white") .append("title") .text((d) => `Cluster ${d.data.name}\n${format(d.data.value)} phages`); svg .append("g") .selectAll("path") .data(innerArcs) .join("path") .attr("d", innerArc) .attr("fill", (d) => innerColor(d.data.name)) .attr("stroke", "white") .style("cursor", level === "strainDetail" ? "default" : "pointer") .on("click", (event, d) => { if (level === "genus") { mutable selectedGenus = d.data.name; mutable selectedSpecies = null; mutable selectedStrain = null; mutable level = "species"; } else if (level === "species") { mutable selectedSpecies = d.data.name; mutable selectedStrain = null; mutable level = "strain"; } else if (level === "strain") { mutable selectedStrain = d.data.name; mutable level = "strainDetail"; } }) .append("title") .text((d) => `${d.data.name}\n${format(d.data.value)} phages`); svg .append("g") .selectAll("text") .data(innerArcs.filter((d) => d.endAngle - d.startAngle > 0.08)) .join("text") .attr("transform", (d) => `translate(${innerLabelArc.centroid(d)})`) .attr("text-anchor", "middle") .attr("dy", "0.35em") .style("font-size", "11px") .text((d) => d.data.name); svg .append("g") .selectAll("text") .data(outerArcs.filter((d) => d.endAngle - d.startAngle > 0.08)) .join("text") .attr("transform", (d) => `translate(${outerLabelArc.centroid(d)})`) .attr("text-anchor", "middle") .attr("dy", "0.35em") .style("font-size", "11px") .text((d) => d.data.name); const center = svg .append("g") .style("cursor", level === "genus" ? "default" : "pointer") .on("click", () => { if (level === "strainDetail") { mutable level = "strain"; mutable selectedStrain = null; } else if (level === "strain") { mutable level = "species"; mutable selectedSpecies = null; mutable selectedStrain = null; } else if (level === "species") { mutable level = "genus"; mutable selectedGenus = null; mutable selectedSpecies = null; mutable selectedStrain = null; } }); center .append("circle") .attr("r", centerRadius) .attr("fill", "#f3f3f3") .attr("stroke", "#bbb"); const centerTitle = level === "genus" ? "Host genus" : level === "species" ? "Host species" : level === "strain" ? "Host strain" : "Selected strain"; const centerSubtitle = level === "genus" ? "Root" : level === "species" ? selectedGenus : level === "strain" ? selectedSpecies : selectedStrain; center .append("text") .attr("text-anchor", "middle") .attr("y", -12) .style("font-size", "18px") .style("font-weight", 700) .text(centerTitle); center .append("text") .attr("text-anchor", "middle") .attr("y", 10) .style("font-size", "11px") .text(centerSubtitle ?? ""); if (level !== "genus") { center .append("text") .attr("text-anchor", "middle") .attr("y", 30) .style("font-size", "10px") .style("fill", "#666") .text("Click center to go back"); } return svg.node(); }3b:Tc15,makeHostList = () => { const title = level === "genus" ? "Host genera" : level === "species" ? "Host species" : "Host strains"; const selectedName = level === "genus" ? selectedGenus : level === "species" ? selectedSpecies : selectedStrain; const wrap = html`

${title}

Host

Phages

Clusters

`; const options = wrap.querySelector(".options"); for (const d of currentOptions) { const isSelected = d.name === selectedName; const btn = html``; btn.onclick = () => { if (level === "genus") { mutable selectedGenus = d.name; mutable selectedSpecies = null; mutable selectedStrain = null; mutable level = "species"; } else if (level === "species") { mutable selectedSpecies = d.name; mutable selectedStrain = null; mutable level = "strain"; } else { mutable selectedStrain = d.name; mutable level = "strainDetail"; } }; options.append(btn); } return wrap; }3c:T777,getGenomeSequenceFromPhamerator = async function (phageName) { const cacheKey = `${dataset}::${phageName}`; if (phameratorSequenceCache[cacheKey]) { const cached = phameratorSequenceCache[cacheKey]; mutable phameratorDebug = [ ...phameratorDebug, { phage_requested: phageName, tried_names: [phageName], success: true, sequence_length: cached.sequence.length, error: null, source: "cache" } ]; return cached.sequence; } const entry = { phage_requested: phageName, tried_names: [], success: false, sequence_length: 0, error: null, source: "api" }; const namesToTry = [phageName, phageName + "_Draft"]; for (const name of namesToTry) { entry.tried_names.push(name); try { const genome = await getPhameratorData( dataset, `/genome/${name}`, user.email, user.password ); const sequence = (genome.sequence ?? "") .toString() .replace(/\s+/g, "") .replace(/[^A-Za-z]/g, "") .toUpperCase() .trim(); entry.sequence_length = sequence.length; if (!sequence) { entry.error = "Sequence empty"; continue; } entry.success = true; const updatedCache = { ...phameratorSequenceCache, [cacheKey]: { phage_requested: phageName, resolved_name: name, sequence } }; localStorage.setItem( phameratorSequenceCacheKey, JSON.stringify(updatedCache) ); mutable phameratorSequenceCache = updatedCache; mutable phameratorDebug = [...phameratorDebug, entry]; return sequence; } catch (err) { entry.error = err.message; } } mutable phameratorDebug = [...phameratorDebug, entry]; throw new Error(entry.error || "All name attempts failed"); }3d:[] 2c:{"id":"08356a947e7a3030","slug":"clusters-by-host","title":"Clusters by Host Genus, Species, & Strain","thumbnail":"ac656f4bb2445fed649f5194474ab76d28a1e7e90a56ea6c090e0cb32bdfb775","access_level":"public","create_time":"$D2026-03-24T13:08:48.771Z","update_time":"$D2026-04-02T19:27:22.983Z","view_time":null,"first_public_time":"$D2026-03-24T19:25:37.965Z","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":412,"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":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"title":"Clusters by Host Genus, Species, & Strain","cells":[{"id":0,"value":"# Clusters by Host Genus, Species, & Strain","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":186,"value":"$2e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":45,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":55,"value":"app = {\n const wrap = html`\n

\n\n

\n `;\n\n wrap.querySelector(\".chart-slot\").appendChild(makeChart());\n wrap.querySelector(\".list-slot\").appendChild(makeHostList());\n\n return wrap;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":35,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":239,"value":"## Download Host Selected Phage FASTAs","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":272,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":332,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":403,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":391,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":230,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":395,"value":"$36","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4,"value":"---\n# Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":137,"value":"#### Tracks the current navigation level in the hierarchy (genus → species → strain → strainDetail)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":6,"value":"mutable level = \"genus\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":141,"value":"#### Stores the currently selected host genus, species, and strain for drill-down navigation","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10,"value":"mutable selectedGenus = null","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8,"value":"mutable selectedSpecies = null","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"mutable selectedStrain = null","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":143,"value":"#### Defines the localStorage key used to cache phage data between sessions","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":16,"value":"cacheKey = \"phagesdb-cache-v1\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":19,"value":"cachedPhages = {\n const raw = localStorage.getItem(cacheKey);\n return raw ? JSON.parse(raw) : {updatedAt: null, phages: []};\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":145,"value":"#### Loads cached phage data (if available) from localStorage","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":21,"value":"mutable phages = cachedPhages.phages","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":23,"value":"mutable cacheUpdatedAt = cachedPhages.updatedAt","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":147,"value":"#### Fetches all phage data from PhagesDB API, including cluster, host, and metadata fields","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":25,"value":"$37","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":149,"value":"#### Utility functions to detect newly added or updated phages compared to cached data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":27,"value":"hasNewPhages = function (oldRows, newRows) {\n const oldNames = new Set(oldRows.map(d => d.phage_name));\n return newRows.some(d => !oldNames.has(d.phage_name));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":29,"value":"hasModifiedPhages = function (oldRows, newRows) {\n const oldMap = new Map(oldRows.map(d => [d.phage_name, d.date_modified ?? \"\"]));\n return newRows.some(d => (oldMap.get(d.phage_name) ?? \"\") !== (d.date_modified ?? \"\"));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":151,"value":"#### Stores the result of the last data update (e.g., updated, unchanged, or error)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":33,"value":"mutable updateResult = null","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":153,"value":"#### Filters phage dataset based on the current selection level (genus, species, or strain)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":37,"value":"selectedRows = {\n const rows = normalizedPhages ?? [];\n\n return rows.filter((d) => {\n const genusOk =\n !selectedGenera.length || selectedGenera.includes(d.host_genus);\n\n const speciesOk =\n !selectedSpeciesList.length ||\n selectedSpeciesList.includes(d.host_species);\n\n const strainOk =\n !selectedStrainsList.length ||\n selectedStrainsList.includes(d.host_strain);\n\n return genusOk && speciesOk && strainOk;\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":155,"value":"#### Aggregates data for inner ring of the chart (hosts at current level)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":39,"value":"$38","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":162,"value":"#### Aggregates data for outer ring of the chart (phage clusters for selected hosts)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":41,"value":"outerData = {\n return [...d3.rollup(selectedRows, v => v.length, d => d.cluster)]\n .map(([name, value]) => ({name, value}))\n .sort((a, b) => d3.descending(a.value, b.value));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":159,"value":"#### Computes summary statistics (phages, clusters, subclusters, names) for the current selection","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":43,"value":"$39","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":164,"value":"#### Generates list of selectable hosts (genus, species, or strain) with phage and cluster counts","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":49,"value":"currentOptions = {\n const getGenus = (d) => d.genus ?? d.host_genus ?? \"\";\n const getSpecies = (d) => d.species ?? d.host_species ?? \"\";\n const getStrain = (d) => d.strain ?? d.host_strain ?? \"\";\n\n let grouped;\n\n if (level === \"genus\") {\n grouped = d3.groups(phages, (d) => getGenus(d));\n } else if (level === \"species\") {\n grouped = d3.groups(\n phages.filter((d) => getGenus(d) === selectedGenus),\n (d) => getSpecies(d)\n );\n } else {\n grouped = d3.groups(\n phages.filter((d) => getSpecies(d) === selectedSpecies),\n (d) => getStrain(d)\n );\n }\n\n return grouped\n .filter(([name]) => !!name)\n .map(([name, rows]) => ({\n name,\n phages: rows.length,\n clusters: new Set(rows.map((d) => d.cluster).filter(Boolean)).size\n }))\n .sort((a, b) => d3.ascending(a.name, b.name));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":166,"value":"#### Creates interactive sunburst chart showing host hierarchy and associated phage clusters","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":51,"value":"$3a","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":168,"value":"#### Renders interactive list of hosts with phage and cluster counts for navigation","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":53,"value":"$3b","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":234,"value":"### Get Phamerator Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":236,"value":"$3c","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":270,"value":"import {\n terms,\n getPhameratorData,\n user,\n formWithSubmit,\n styles\n} with { formData } from \"@scresawn/phamerator-api-utilities\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":341,"value":"normalizedPhages = (phages ?? []).map((d) => {\n const host_genus = d.genus ?? d.host_genus ?? \"\";\n const host_species = d.species ?? d.host_species ?? \"\";\n const host_strain = d.strain ?? d.host_strain ?? \"\";\n\n return {\n ...d,\n host_genus,\n host_species,\n host_strain,\n genus: host_genus,\n species: host_species,\n strain: host_strain,\n cluster: d.cluster ?? \"Unknown\",\n subcluster: d.subcluster ?? \"\",\n phage_name: d.phage_name ?? \"\",\n institution: d.institution ?? \"\",\n institution_name: d.institution_name ?? \"\"\n };\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":349,"value":"phameratorSequenceCacheKey = \"phamerator-sequence-cache-v1\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":351,"value":"mutable phameratorSequenceCache = {\n const raw = localStorage.getItem(phameratorSequenceCacheKey);\n return raw ? JSON.parse(raw) : {};\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":353,"value":"mutable phameratorDebug = []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":361,"value":"mutable selectedGenera = []","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":364,"value":"mutable selectedSpeciesList = []","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":366,"value":"mutable selectedStrainsList = []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W3d","stdlib":"1","titling":"auto"}} 2d:"$2c:body"