28:null 29:["$","title",null,{"children":"Download Genomes by Host or Cluster | WabushOnce | Observable"}] 2e:Tc09,viewof fastaBackupControl = { const wrap = html`

`; const statusNode = wrap.querySelector(".status"); const actionsNode = wrap.querySelector(".actions"); const buttonStyle = ` padding:6px 12px; border:1px solid #ccc; border-radius:8px; background:white; cursor:pointer; font:13px sans-serif; color:#222; text-decoration:none; display:inline-block; `; const downloadLink = html`Download PhagesDB multifasta`; const uploadLabel = html` Upload multifasta file `; const fileInput = uploadLabel.querySelector("input"); const actionStatus = html``; downloadLink.onmouseenter = () => (downloadLink.style.background = "#f5f5f5"); downloadLink.onmouseleave = () => (downloadLink.style.background = "white"); uploadLabel.onmouseenter = () => (uploadLabel.style.background = "#f5f5f5"); uploadLabel.onmouseleave = () => (uploadLabel.style.background = "white"); function renderStatus(file) { statusNode.replaceChildren(html`

Back-up DNA sequence source

Use the PhagesDB multifasta file containing all sequenced phage genomes as a backup source for DNA sequences.

Download the multifasta file from PhagesDB, then upload it here so the notebook can match phage names to sequences locally.

${ file ? html`

Uploaded file: ${file.name}

` : html`

No multifasta file uploaded yet.

` }

`); } fileInput.onchange = async () => { const file = fileInput.files?.[0] ?? null; wrap.value = file; renderStatus(file); actionStatus.textContent = file ? `Ready: ${file.name}` : "No file selected"; wrap.dispatchEvent(new CustomEvent("input")); }; actionsNode.append(downloadLink, uploadLabel, actionStatus); wrap.value = null; renderStatus(null); return wrap; }2f:T18a6,cacheStatus2 = { 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``; const checkBtn = html``; const actionStatus = html``; updateBtn.onmouseenter = () => (updateBtn.style.background = "#f5f5f5"); updateBtn.onmouseleave = () => (updateBtn.style.background = "white"); checkBtn.onmouseenter = () => (checkBtn.style.background = "#f5f5f5"); checkBtn.onmouseleave = () => (checkBtn.style.background = "white"); async function fetchSequencedPhageCount() { const response = await fetch( "https://phagesdb.org/api/sequenced_phages/?page=1&page_size=1" ); if (!response.ok) { throw new Error(`PhagesDB returned ${response.status}`); } const data = await response.json(); return data.count ?? 0; } const localCount = phages.length; const lastSynced = cacheUpdatedAt ? new Date(cacheUpdatedAt).toLocaleString() : "Never"; let remoteCount = null; let remoteError = null; try { remoteCount = await fetchSequencedPhageCount(); } catch (err) { remoteError = err.message; } const difference = remoteCount == null ? null : remoteCount - localCount; function statusBlock() { return html`

PhagesDB data is stored locally to save download time.

Last synced on ${lastSynced} and contains ${localCount} phages.

${ remoteError ? html`

Could not check the current number of sequenced phages on PhagesDB.

` : html`

PhagesDB currently lists ${remoteCount} sequenced phages.

${ difference === 0 ? html`

Your local PhagesDB data appears to be up to date.

` : html`

The local PhagesDB data appears to be out of date. Please Refresh the PhagesDB data.

` } ` } ${ updateResult ? html`

Last refresh check: ${ updateResult.error ? "there was an error while checking for updates." : updateResult.updated ? `the local cache was refreshed and now contains ${updateResult.count} phages.` : `no changes were found after checking ${updateResult.count} phages.` }

` : "" }

`; } updateBtn.onclick = async () => { updateBtn.textContent = "Refreshing..."; updateBtn.disabled = true; checkBtn.disabled = true; actionStatus.textContent = ""; 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 = "Refresh PhagesDB data"; updateBtn.disabled = false; checkBtn.disabled = false; }; checkBtn.onclick = async () => { checkBtn.textContent = "Checking..."; checkBtn.disabled = true; updateBtn.disabled = true; actionStatus.textContent = ""; try { const currentRemote = await fetchSequencedPhageCount(); const currentLocal = phages.length; const diff = currentRemote - currentLocal; actionStatus.textContent = diff === 0 ? `PhagesDB count matches local cache (${currentRemote}).` : `PhagesDB has ${currentRemote}; local cache has ${currentLocal}. Please Refresh the PhagesDB data.`; } catch (err) { actionStatus.textContent = "Could not check the current PhagesDB count."; } checkBtn.textContent = "Check PhagesDB count"; checkBtn.disabled = false; updateBtn.disabled = false; }; wrap.querySelector(".status").append(statusBlock()); wrap.querySelector(".actions").append(updateBtn, checkBtn, actionStatus); return wrap; }30:T54d,display = { const totalPhages = normalizedPhages.length; const totalClusters = new Set( normalizedPhages.map((d) => d.cluster).filter(Boolean) ).size; const totalSubclusters = new Set( normalizedPhages.map((d) => d.subcluster).filter(Boolean) ).size; const totalInstitutions = new Set( normalizedPhages.map((d) => d.institution_name).filter(Boolean) ).size; const pct = (value, total) => total > 0 ? `${((100 * value) / total).toFixed(1)}%` : "0.0%"; return html`

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

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

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

Institutions: ${ summary.institutions } / ${totalInstitutions} (${pct( summary.institutions, totalInstitutions )})

`; } 31:T44ad,controls = { const rows = normalizedPhages ?? []; const getGenus = (d) => d.host_genus ?? d.genus ?? ""; const getSpecies = (d) => d.host_species ?? d.species ?? ""; const getStrain = (d) => d.host_strain ?? d.strain ?? ""; const getCluster = (d) => d.cluster ?? ""; const getSubcluster = (d) => d.subcluster ?? ""; const getInstitution = (d) => d.institution_name ?? ""; function speciesLabel(value) { const species = (value ?? "").trim(); if (!species) return ""; const parts = species.split(/\s+/); return parts.length > 1 ? parts.slice(1).join(" ") : species; } let genusSearch = ""; let speciesSearch = ""; let strainSearch = ""; let clusterSearch = ""; let subclusterSearch = ""; let institutionSearch = ""; const wrap = html`

`; const modeSlot = wrap.querySelector(".mode"); const actionSlot = wrap.querySelector(".actions"); const filtersSlot = wrap.querySelector(".filters"); const buttonStyle = ` padding:6px 12px; border:1px solid #ccc; border-radius:8px; background:white; cursor:pointer; font:13px sans-serif; white-space:nowrap; `; const miniButtonStyle = ` border:1px solid #ddd; background:white; border-radius:6px; padding:2px 6px; font-size:11px; cursor:pointer; white-space:nowrap; `; const selectStyle = ` padding:6px 8px; border:1px solid #ccc; border-radius:8px; background:white; font:12px sans-serif; width:100%; min-height:115px; box-sizing:border-box; `; const inputStyle = ` padding:5px 7px; border:1px solid #ccc; border-radius:8px; background:white; font:12px sans-serif; width:100%; max-width:100%; box-sizing:border-box; `; function makeBox(labelText, width = 170) { return html`

${labelText}

`; } function fillMultiSelect( select, options, selectedValues, labelFn = (v) => v ) { const current = new Set(selectedValues); select.innerHTML = ""; for (const value of options) { const option = html``; option.selected = current.has(value); select.append(option); } } function getSelected(select) { return [...select.selectedOptions].map((o) => o.value); } function setCount(box, selectedValues, options) { box.querySelector( ".count" ).textContent = `${selectedValues.length} selected / ${options.length} total`; } function filterBySearch(options, term, labelFn = (v) => v) { const q = term.trim().toLowerCase(); return q ? options.filter((v) => labelFn(v).toLowerCase().includes(q)) : options; } function makeActionButton(label, onClick) { const btn = html``; btn.onmouseenter = () => (btn.style.background = "#f5f5f5"); btn.onmouseleave = () => (btn.style.background = "white"); btn.onclick = onClick; return btn; } function addMiniActions(box, getVisibleOptions, setCurrent) { const slot = box.querySelector(".mini-actions"); const allBtn = html``; const noneBtn = html``; allBtn.onclick = (e) => { e.preventDefault(); setCurrent(getVisibleOptions().slice()); syncControls(); }; noneBtn.onclick = (e) => { e.preventDefault(); setCurrent([]); syncControls(); }; slot.append(allBtn, noneBtn); } function baseInstitutionRows() { return rows.filter((d) => { if (filterMode === "host") { const genusOk = !selectedGenera.length || selectedGenera.includes(getGenus(d)); const speciesOk = !selectedSpeciesList.length || selectedSpeciesList.includes(getSpecies(d)); const strainOk = !selectedStrainsList.length || selectedStrainsList.includes(getStrain(d)); return genusOk && speciesOk && strainOk; } const clusterOk = !selectedClusters.length || selectedClusters.includes(getCluster(d)); const subclusterOk = !selectedSubclusters.length || selectedSubclusters.includes(getSubcluster(d)); return clusterOk && subclusterOk; }); } const modeForm = html` `; modeForm.addEventListener("change", () => { mutable filterMode = modeForm.querySelector('input[name="filter-mode"]:checked')?.value ?? "host"; syncControls(); }); const clearHostBtn = makeActionButton("Clear host", () => { mutable selectedGenera = []; mutable selectedSpeciesList = []; mutable selectedStrainsList = []; syncControls(); }); const clearClusterBtn = makeActionButton("Clear cluster", () => { mutable selectedClusters = []; mutable selectedSubclusters = []; syncControls(); }); const clearInstitutionBtn = makeActionButton("Clear institution", () => { mutable selectedInstitutions = []; syncControls(); }); const resetBtn = makeActionButton("Clear all", () => { mutable selectedGenera = []; mutable selectedSpeciesList = []; mutable selectedStrainsList = []; mutable selectedClusters = []; mutable selectedSubclusters = []; mutable selectedInstitutions = []; syncControls(); }); modeSlot.append(modeForm); actionSlot.append( clearHostBtn, clearClusterBtn, clearInstitutionBtn, resetBtn ); const genusBox = makeBox("Host genus", 160); const speciesBox = makeBox("Host species", 180); const strainBox = makeBox("Host strain", 180); const clusterBox = makeBox("Cluster", 145); const subclusterBox = makeBox("Subcluster", 145); const institutionBox = makeBox("Institution", 280); const genusSearchInput = genusBox.querySelector(".search"); const speciesSearchInput = speciesBox.querySelector(".search"); const strainSearchInput = strainBox.querySelector(".search"); const clusterSearchInput = clusterBox.querySelector(".search"); const subclusterSearchInput = subclusterBox.querySelector(".search"); const institutionSearchInput = institutionBox.querySelector(".search"); const genusSelect = genusBox.querySelector("select"); const speciesSelect = speciesBox.querySelector("select"); const strainSelect = strainBox.querySelector("select"); const clusterSelect = clusterBox.querySelector("select"); const subclusterSelect = subclusterBox.querySelector("select"); const institutionSelect = institutionBox.querySelector("select"); genusSearchInput.oninput = () => { genusSearch = genusSearchInput.value; syncControls(); genusSearchInput.focus(); genusSearchInput.setSelectionRange(genusSearch.length, genusSearch.length); }; speciesSearchInput.oninput = () => { speciesSearch = speciesSearchInput.value; syncControls(); speciesSearchInput.focus(); speciesSearchInput.setSelectionRange( speciesSearch.length, speciesSearch.length ); }; strainSearchInput.oninput = () => { strainSearch = strainSearchInput.value; syncControls(); strainSearchInput.focus(); strainSearchInput.setSelectionRange( strainSearch.length, strainSearch.length ); }; clusterSearchInput.oninput = () => { clusterSearch = clusterSearchInput.value; syncControls(); clusterSearchInput.focus(); clusterSearchInput.setSelectionRange( clusterSearch.length, clusterSearch.length ); }; subclusterSearchInput.oninput = () => { subclusterSearch = subclusterSearchInput.value; syncControls(); subclusterSearchInput.focus(); subclusterSearchInput.setSelectionRange( subclusterSearch.length, subclusterSearch.length ); }; institutionSearchInput.oninput = () => { institutionSearch = institutionSearchInput.value; syncControls(); institutionSearchInput.focus(); institutionSearchInput.setSelectionRange( institutionSearch.length, institutionSearch.length ); }; genusSelect.onchange = () => { mutable selectedGenera = getSelected(genusSelect); syncControls(); }; speciesSelect.onchange = () => { mutable selectedSpeciesList = getSelected(speciesSelect); syncControls(); }; strainSelect.onchange = () => { mutable selectedStrainsList = getSelected(strainSelect); syncControls(); }; clusterSelect.onchange = () => { mutable selectedClusters = getSelected(clusterSelect); const allowedSubclusters = selectedClusters.length ? new Set( rows .filter((d) => selectedClusters.includes(getCluster(d))) .map(getSubcluster) .filter(Boolean) ) : null; if (allowedSubclusters) { mutable selectedSubclusters = selectedSubclusters.filter((v) => allowedSubclusters.has(v) ); } syncControls(); }; subclusterSelect.onchange = () => { mutable selectedSubclusters = getSelected(subclusterSelect); syncControls(); }; institutionSelect.onchange = () => { mutable selectedInstitutions = getSelected(institutionSelect); syncControls(); }; addMiniActions( genusBox, () => filterBySearch( [...new Set(rows.map(getGenus).filter(Boolean))].sort(d3.ascending), genusSearch ), (vals) => (mutable selectedGenera = vals) ); addMiniActions( speciesBox, () => { const base = selectedGenera.length ? rows.filter((d) => selectedGenera.includes(getGenus(d))) : rows; return filterBySearch( [...new Set(base.map(getSpecies).filter(Boolean))].sort(d3.ascending), speciesSearch, speciesLabel ); }, (vals) => (mutable selectedSpeciesList = vals) ); addMiniActions( strainBox, () => { const base = selectedSpeciesList.length ? rows.filter((d) => selectedSpeciesList.includes(getSpecies(d))) : selectedGenera.length ? rows.filter((d) => selectedGenera.includes(getGenus(d))) : rows; return filterBySearch( [...new Set(base.map(getStrain).filter(Boolean))].sort(d3.ascending), strainSearch ); }, (vals) => (mutable selectedStrainsList = vals) ); addMiniActions( clusterBox, () => filterBySearch( [...new Set(rows.map(getCluster).filter(Boolean))].sort(d3.ascending), clusterSearch ), (vals) => (mutable selectedClusters = vals) ); addMiniActions( subclusterBox, () => { const base = selectedClusters.length ? rows.filter((d) => selectedClusters.includes(getCluster(d))) : rows; return filterBySearch( [...new Set(base.map(getSubcluster).filter(Boolean))].sort( d3.ascending ), subclusterSearch ); }, (vals) => (mutable selectedSubclusters = vals) ); addMiniActions( institutionBox, () => filterBySearch( [ ...new Set(baseInstitutionRows().map(getInstitution).filter(Boolean)) ].sort(d3.ascending), institutionSearch ), (vals) => (mutable selectedInstitutions = vals) ); filtersSlot.append( genusBox, speciesBox, strainBox, clusterBox, subclusterBox, institutionBox ); function syncControls() { const genusOptions = filterBySearch( [...new Set(rows.map(getGenus).filter(Boolean))].sort(d3.ascending), genusSearch ); const genusSelectedVisible = selectedGenera.filter((v) => genusOptions.includes(v) ); fillMultiSelect(genusSelect, genusOptions, genusSelectedVisible); setCount(genusBox, genusSelectedVisible, genusOptions); const speciesBase = selectedGenera.length ? rows.filter((d) => selectedGenera.includes(getGenus(d))) : rows; const speciesOptions = filterBySearch( [...new Set(speciesBase.map(getSpecies).filter(Boolean))].sort( d3.ascending ), speciesSearch, speciesLabel ); const speciesSelectedVisible = selectedSpeciesList.filter((v) => speciesOptions.includes(v) ); fillMultiSelect( speciesSelect, speciesOptions, speciesSelectedVisible, speciesLabel ); setCount(speciesBox, speciesSelectedVisible, speciesOptions); const strainBase = selectedSpeciesList.length ? rows.filter((d) => selectedSpeciesList.includes(getSpecies(d))) : selectedGenera.length ? rows.filter((d) => selectedGenera.includes(getGenus(d))) : rows; const strainOptions = filterBySearch( [...new Set(strainBase.map(getStrain).filter(Boolean))].sort( d3.ascending ), strainSearch ); const strainSelectedVisible = selectedStrainsList.filter((v) => strainOptions.includes(v) ); fillMultiSelect(strainSelect, strainOptions, strainSelectedVisible); setCount(strainBox, strainSelectedVisible, strainOptions); const clusterOptions = filterBySearch( [...new Set(rows.map(getCluster).filter(Boolean))].sort(d3.ascending), clusterSearch ); const clusterSelectedVisible = selectedClusters.filter((v) => clusterOptions.includes(v) ); fillMultiSelect(clusterSelect, clusterOptions, clusterSelectedVisible); setCount(clusterBox, clusterSelectedVisible, clusterOptions); const subclusterBase = selectedClusters.length ? rows.filter((d) => selectedClusters.includes(getCluster(d))) : rows; const subclusterOptions = filterBySearch( [...new Set(subclusterBase.map(getSubcluster).filter(Boolean))].sort( d3.ascending ), subclusterSearch ); const subclusterSelectedVisible = selectedSubclusters.filter((v) => subclusterOptions.includes(v) ); fillMultiSelect( subclusterSelect, subclusterOptions, subclusterSelectedVisible ); setCount(subclusterBox, subclusterSelectedVisible, subclusterOptions); const institutionOptions = filterBySearch( [ ...new Set(baseInstitutionRows().map(getInstitution).filter(Boolean)) ].sort(d3.ascending), institutionSearch ); const institutionSelectedVisible = selectedInstitutions.filter((v) => institutionOptions.includes(v) ); fillMultiSelect( institutionSelect, institutionOptions, institutionSelectedVisible ); setCount(institutionBox, institutionSelectedVisible, institutionOptions); if (filterMode === "host") { genusBox.style.display = ""; speciesBox.style.display = ""; strainBox.style.display = ""; clusterBox.style.display = "none"; subclusterBox.style.display = "none"; institutionBox.style.display = ""; } else { genusBox.style.display = "none"; speciesBox.style.display = "none"; strainBox.style.display = "none"; clusterBox.style.display = ""; subclusterBox.style.display = ""; institutionBox.style.display = ""; } } syncControls(); return wrap; }32:Ta3b,viewof fastaDownloadPanel = { const rows = selectedRows ?? []; function pickPhages(rows, mode) { const sorted = (rows ?? []) .slice() .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)); if (mode === "all") { return sorted; } if (mode === "cluster") { return d3 .groups(sorted, (d) => d.cluster || "Unknown") .map(([, group]) => group[0]) .filter(Boolean); } return d3 .groups( sorted, (d) => d.cluster || "Unknown", (d) => d.subcluster && d.subcluster.trim() !== "" ? d.subcluster : "__NO_SUBCLUSTER__" ) .flatMap(([, subgroups]) => subgroups.map(([, group]) => group[0]).filter(Boolean) ); } function modeCounts() { return { all: pickPhages(rows, "all").length, cluster: pickPhages(rows, "cluster").length, cluster_subcluster: pickPhages(rows, "cluster_subcluster").length }; } const counts = modeCounts(); const wrap = html`

Phage selection mode

Show: All phages (${counts.all}) Representative per cluster (${counts.cluster}) Representative per cluster + subcluster (${counts.cluster_subcluster})

`; function currentSettings() { return { downloadMode: wrap.querySelector('input[name="download-mode"]:checked')?.value ?? "all" }; } function updateValue() { wrap.value = currentSettings(); wrap.dispatchEvent(new CustomEvent("input")); } wrap.addEventListener("change", updateValue); updateValue(); return wrap; }33:T2db2,viewof resultsTable = { const allRows = (filteredPhageRows ?? []).slice(); const wrap = html`

Results (${downloadMode})

`; const searchInput = wrap.querySelector(".search"); const selectVisibleBtn = wrap.querySelector(".select-visible-btn"); const clearSelectedBtn = wrap.querySelector(".clear-selected-btn"); const csvBtn = wrap.querySelector(".csv-btn"); const tsvBtn = wrap.querySelector(".tsv-btn"); const copyBtn = wrap.querySelector(".copy-btn"); const exportStatus = wrap.querySelector(".export-status"); const summaryNode = wrap.querySelector(".summary"); const tableWrap = wrap.querySelector(".table-wrap"); let sortKey = "phage_name"; let sortDir = "asc"; let searchTerm = ""; // Store selected phage names. const selectedPhageNames = new Set(); function clean(value) { return (value ?? "") .toString() .trim() .replace(/\s+/g, "_") .replace(/[^A-Za-z0-9._-]/g, "_"); } function speciesOnly(d) { const species = (d.host_species ?? "").trim(); const genus = (d.host_genus ?? "").trim(); if (genus && species.startsWith(genus + " ")) { return species.slice(genus.length + 1); } return species; } function searchedRows(rows) { const q = searchTerm.toLowerCase().trim(); if (!q) return rows; return rows.filter( (d) => (d.phage_name ?? "").toLowerCase().includes(q) || (d.cluster ?? "").toLowerCase().includes(q) || (d.subcluster ?? "").toLowerCase().includes(q) || (d.host_genus ?? "").toLowerCase().includes(q) || speciesOnly(d).toLowerCase().includes(q) || (d.host_strain ?? "").toLowerCase().includes(q) ); } function sortRows(data) { return data.slice().sort((a, b) => { const valA = sortKey === "species_only" ? speciesOnly(a) : a[sortKey]; const valB = sortKey === "species_only" ? speciesOnly(b) : b[sortKey]; const result = d3.ascending(valA ?? "", valB ?? ""); return sortDir === "asc" ? result : -result; }); } function currentShownRows() { return sortRows(searchedRows(allRows)); } function selectedRows() { return allRows.filter((d) => selectedPhageNames.has(d.phage_name)); } function updateValue() { const rows = selectedRows(); wrap.value = { selectedRows: rows, selectedPhageNames: rows.map((d) => d.phage_name), selectedCount: rows.length }; wrap.dispatchEvent(new CustomEvent("input")); } function headerCell(label, key) { const isActive = sortKey === key; const arrow = isActive ? (sortDir === "asc" ? " ▲" : " ▼") : ""; const th = html`${label}${arrow}`; th.onclick = () => { if (sortKey === key) { sortDir = sortDir === "asc" ? "desc" : "asc"; } else { sortKey = key; sortDir = "asc"; } render(); }; return th; } function exportRows(format) { const rows = sortRows(searchedRows(allRows)); if (!rows.length) { exportStatus.textContent = "No rows to export."; return; } const sep = format === "tsv" ? "\t" : ","; const escapeValue = (value) => { const s = (value ?? "").toString(); if (format === "tsv") return s.replace(/\t/g, " "); return `"${s.replace(/"/g, '""')}"`; }; const lines = [ ["selected", "phage", "cluster", "subcluster", "genus", "species", "strain"] .map(escapeValue) .join(sep), ...rows.map((d) => [ escapeValue(selectedPhageNames.has(d.phage_name) ? "yes" : "no"), escapeValue(d.phage_name), escapeValue(d.cluster), escapeValue(d.subcluster || ""), escapeValue(d.host_genus || ""), escapeValue(speciesOnly(d)), escapeValue(d.host_strain || "") ].join(sep) ) ]; if (format === "copy") { navigator.clipboard.writeText(lines.join("\n")); exportStatus.textContent = `Copied ${rows.length} rows.`; return; } const fileName = clean(`results_${downloadMode}_${rows.length}_rows`) + `.${format}`; const mime = format === "csv" ? "text/csv;charset=utf-8" : "text/tab-separated-values;charset=utf-8"; const blob = new Blob([lines.join("\n")], { type: mime }); const url = URL.createObjectURL(blob); const a = html``; document.body.appendChild(a); a.click(); a.remove(); URL.revokeObjectURL(url); exportStatus.textContent = `Downloaded ${rows.length} rows as ${format.toUpperCase()}.`; } function render() { const shown = currentShownRows(); const selectedCount = selectedPhageNames.size; summaryNode.textContent = `Showing ${shown.length} of ${allRows.length} rows; ${selectedCount} selected for FASTA download`; const table = html`

`; const thead = html``; const tbody = html``; const selectHeader = html`Use`; thead .querySelector("tr") .append( selectHeader, headerCell("Phage", "phage_name"), headerCell("Cluster", "cluster"), headerCell("Subcluster", "subcluster"), headerCell("Genus", "host_genus"), headerCell("Species", "species_only"), headerCell("Strain", "host_strain") ); for (const d of shown) { const tr = html``; const checkbox = html``; checkbox.checked = selectedPhageNames.has(d.phage_name); checkbox.onchange = () => { if (checkbox.checked) { selectedPhageNames.add(d.phage_name); } else { selectedPhageNames.delete(d.phage_name); } updateValue(); render(); }; tr.append( html`${checkbox}`, html` ${d.phage_name} `, html`${d.cluster ?? ""}`, html`${d.subcluster ?? ""}`, html`${d.host_genus ?? ""}`, html`${speciesOnly(d)}`, html`${d.host_strain ?? ""}` ); tbody.append(tr); } table.append(thead, tbody); tableWrap.replaceChildren(table); } searchInput.oninput = () => { searchTerm = searchInput.value; render(); }; selectVisibleBtn.onclick = () => { for (const d of currentShownRows()) { if (d.phage_name) selectedPhageNames.add(d.phage_name); } updateValue(); render(); }; clearSelectedBtn.onclick = () => { selectedPhageNames.clear(); updateValue(); render(); }; csvBtn.onclick = () => exportRows("csv"); tsvBtn.onclick = () => exportRows("tsv"); copyBtn.onclick = () => exportRows("copy"); updateValue(); render(); return wrap; }34:T2fb4,viewof fastaHeaderPanel = { const rows = selectedRows ?? []; function pickPhages(rows, mode) { const sorted = (rows ?? []) .slice() .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)); if (mode === "all") return sorted; if (mode === "cluster") { return d3 .groups(sorted, (d) => d.cluster || "Unknown") .map(([, g]) => g[0]) .filter(Boolean); } return d3 .groups( sorted, (d) => d.cluster || "Unknown", (d) => d.subcluster && d.subcluster.trim() !== "" ? d.subcluster : "__NO_SUBCLUSTER__" ) .flatMap(([, subs]) => subs.map(([, g]) => g[0]).filter(Boolean)); } function clean(value) { return (value ?? "") .toString() .trim() .replace(/\s+/g, "_") .replace(/[^A-Za-z0-9._-]/g, "_"); } function wrapSequence(seq, lineLength = 80) { const s = (seq ?? "").replace(/\s+/g, "").toUpperCase(); const lines = []; for (let i = 0; i < s.length; i += lineLength) { lines.push(s.slice(i, i + lineLength)); } return lines.join("\n"); } function getRows() { return downloadRowsFromResultsTable ?? []; } function findSequenceRecord(phageName) { if (!phageName || !allResolvedPhageSequences) return null; const direct = allResolvedPhageSequences.get(phageName); if (direct?.sequence) return direct; const target = normalizePhageName(phageName); for (const [key, value] of allResolvedPhageSequences.entries()) { if (normalizePhageName(key) === target && value?.sequence) { return value; } } return null; } function getHeaderSettings() { const includeCluster = wrap.querySelector(".include-cluster")?.checked ?? true; const includeSubcluster = wrap.querySelector(".include-subcluster")?.checked ?? true; const includePhage = wrap.querySelector(".include-phage")?.checked ?? true; const clusterOrder = Number( wrap.querySelector(".order-cluster")?.value ?? 1 ); const subclusterOrder = Number( wrap.querySelector(".order-subcluster")?.value ?? 2 ); const phageOrder = Number(wrap.querySelector(".order-phage")?.value ?? 3); return { includeCluster, includeSubcluster, includePhage, clusterOrder, subclusterOrder, phageOrder }; } function buildHeaderParts(row, settings) { const parts = []; if (settings.includeCluster) { parts.push({ key: "cluster", order: settings.clusterOrder, value: clean(row.cluster || "Unknown") }); } if (settings.includeSubcluster) { parts.push({ key: "subcluster", order: settings.subclusterOrder, value: row.subcluster && row.subcluster.trim() !== "" ? clean(row.subcluster) : "NA" }); } if (settings.includePhage) { parts.push({ key: "phage", order: settings.phageOrder, value: clean(row.phage_name || "UnknownPhage") }); } return parts .sort((a, b) => a.order - b.order || d3.ascending(a.key, b.key)) .map((d) => d.value) .filter(Boolean); } function buildHeader(row, settings) { const parts = buildHeaderParts(row, settings); if (!parts.length) { return `>${clean(row.phage_name || "UnknownPhage")}`; } return `>${parts.join("_")}`; } function buildFastaText(selectedRows, headerSettings) { const found = []; const missing = []; for (const row of selectedRows) { const phageName = row?.phage_name; const rec = findSequenceRecord(phageName); if (rec?.sequence) { found.push( `${buildHeader(row, headerSettings)}\n${wrapSequence(rec.sequence)}` ); } else { missing.push(phageName); } } return { fastaText: found.join("\n"), foundCount: found.length, missing }; } function downloadTextFile(text, filename, mime = "text/plain;charset=utf-8") { const blob = new Blob([text], { type: mime }); const url = URL.createObjectURL(blob); const a = html``; document.body.appendChild(a); a.click(); a.remove(); URL.revokeObjectURL(url); } function headerPreview(settings) { const sampleRow = getRows()[0] ?? { cluster: "A", subcluster: "A1", phage_name: "20ES" }; return buildHeader(sampleRow, settings); } function normalizeOrders() { const selectCluster = wrap.querySelector(".order-cluster"); const selectSubcluster = wrap.querySelector(".order-subcluster"); const selectPhage = wrap.querySelector(".order-phage"); const values = [ Number(selectCluster.value), Number(selectSubcluster.value), Number(selectPhage.value) ]; const uniqueCount = new Set(values).size; if (uniqueCount === 3) return; const selects = [ { el: selectCluster, name: "cluster" }, { el: selectSubcluster, name: "subcluster" }, { el: selectPhage, name: "phage" } ]; const used = new Set(); for (const s of selects) { let v = Number(s.el.value); if (!used.has(v)) { used.add(v); continue; } for (const candidate of [1, 2, 3]) { if (!used.has(candidate)) { s.el.value = String(candidate); used.add(candidate); break; } } } } const wrap = html`

FASTA header fields

Cluster Order Subcluster Order PhageName Order

Header preview:

Phages to download:

Sequences available:

Missing sequences:

`; const btn = wrap.querySelector(".btn"); const missingBtn = wrap.querySelector(".missing-btn"); const status = wrap.querySelector(".status"); const countNode = wrap.querySelector(".count"); const availableNode = wrap.querySelector(".available-count"); const missingNode = wrap.querySelector(".missing-count"); const previewNode = wrap.querySelector(".preview"); function update() { normalizeOrders(); const selected = getRows(); const settings = getHeaderSettings(); const result = buildFastaText(selected, settings); countNode.textContent = selected.length; availableNode.textContent = result.foundCount; missingNode.textContent = result.missing.length; previewNode.textContent = headerPreview(settings); btn.disabled = !( allResolvedPhageSequences && allResolvedPhageSequences.size > 0 ); btn.style.background = btn.disabled ? "#f3f3f3" : "white"; btn.style.cursor = btn.disabled ? "not-allowed" : "pointer"; if (btn.disabled) { status.textContent = "Upload the multifasta backup file to enable FASTA download."; } else if (result.missing.length) { status.textContent = `Ready to download ${result.foundCount} FASTAs. Missing ${result.missing.length} phage(s).`; } else { status.textContent = `Ready to download ${result.foundCount} FASTAs.`; } wrap.value = { headerSettings: settings, selectedRows: selected, foundCount: result.foundCount, missingPhages: result.missing }; wrap.dispatchEvent(new CustomEvent("input")); } wrap.addEventListener("change", update); btn.onclick = async () => { if (btn.disabled) return; const selected = getRows(); const settings = getHeaderSettings(); const result = buildFastaText(selected, settings); if (!selected.length) { status.textContent = "No phages selected."; return; } if (!result.foundCount) { status.textContent = "No DNA sequences found. Upload the multifasta backup file first."; return; } const filename = clean(`filtered_phages_${downloadMode}_${result.foundCount}`) + ".fasta"; downloadTextFile( result.fastaText + "\n", filename, "text/fasta;charset=utf-8" ); if (result.missing.length) { status.textContent = `Downloaded ${result.foundCount} FASTAs. Missing ${result.missing.length} phage(s).`; } else { status.textContent = `Downloaded ${result.foundCount} FASTAs.`; } }; missingBtn.onclick = () => { const selected = getRows(); const settings = getHeaderSettings(); const result = buildFastaText(selected, settings); if (!result.missing.length) { status.textContent = "No missing phages."; return; } const text = result.missing.join("\n") + "\n"; const filename = clean(`missing_phages_${downloadMode}`) + ".txt"; downloadTextFile(text, filename, "text/plain;charset=utf-8"); status.textContent = `Downloaded missing-phage list (${result.missing.length}).`; }; update(); return wrap; }35:T68e,viewof formData = { const form = html` `; return formWithSubmit(form); }36:Tb90,viewof dataset = { const wrap = html`

Phamerator data set

`; const control = wrap.querySelector(".control"); const note = wrap.querySelector(".note"); function showMessage(message, noteText, value = "Actino_Draft") { control.replaceChildren(html`

${message}

`); note.textContent = noteText; wrap.value = value; return wrap; } Promise.resolve(user).then( (resolvedUser) => { const hasLogin = !!(resolvedUser && resolvedUser.email); const datasets = hasLogin && Array.isArray(resolvedUser.datasets) ? resolvedUser.datasets.slice().sort() : []; if (!hasLogin) { control.replaceChildren(html` `); note.textContent = "The dataset selector will become active after login."; wrap.value = "Actino_Draft"; wrap.dispatchEvent(new CustomEvent("input")); return; } if (datasets.length === 0) { showMessage( "Unable to access Phamerator APIs. The database may be under repair.", "Try again later or use the FASTA backup option." ); wrap.dispatchEvent(new CustomEvent("input")); return; } const initialValue = datasets.includes("Actino_Draft") ? "Actino_Draft" : datasets[0]; const select = Inputs.select(datasets, { value: initialValue }); control.replaceChildren(select); note.textContent = `Available datasets: ${datasets.length}`; wrap.value = select.value; wrap.dispatchEvent(new CustomEvent("input")); select.addEventListener("input", () => { wrap.value = select.value; wrap.dispatchEvent(new CustomEvent("input")); }); }, (err) => { showMessage( "Unable to access Phamerator APIs. The database may be under repair.", "Try again later or use the FASTA backup option." ); wrap.dispatchEvent(new CustomEvent("input")); } ); wrap.value = "Actino_Draft"; return wrap; }37:T8a0,fetchPhagesFromAPI = async function () { const baseUrl = "https://phagesdb.org/api/sequenced_phages/"; const candidates = [2000, 1000, 500, 200]; async function detectPageSize() { for (const size of candidates) { const url = `${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:T61c,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 institutions = [ ...new Set(rows.map((d) => d.institution_name).filter(Boolean)) ].sort(d3.ascending); const phageNames = [ ...new Set(rows.map((d) => d.phage_name).filter(Boolean)) ].sort(d3.ascending); const activeParts = []; if (filterMode === "host") { if (selectedGenera.length) activeParts.push(`Genus: ${selectedGenera.join(", ")}`); if (selectedSpeciesList.length) activeParts.push(`Species: ${selectedSpeciesList.join(", ")}`); if (selectedStrainsList.length) activeParts.push(`Strain: ${selectedStrainsList.join(", ")}`); } else { if (selectedClusters.length) activeParts.push(`Cluster: ${selectedClusters.join(", ")}`); if (selectedSubclusters.length) activeParts.push(`Subcluster: ${selectedSubclusters.join(", ")}`); } if (selectedInstitutions.length) { activeParts.push(`Institution: ${selectedInstitutions.join(", ")}`); } return { selectedLabel: "Active filters", selectedValue: activeParts.length ? activeParts.join(" | ") : "All", phages: rows.length, clusters: clusters.length, subclusters: subclusters.length, institutions: institutions.length, phageNames, clusterNames: clusters, subclusterNames: subclusters, institutionNames: institutions }; }3a:T1767,clusterInsights = { const rows = (normalizedPhages ?? []).filter((d) => d.cluster); function pickPhages(rows, mode) { const sorted = (rows ?? []) .slice() .sort((a, b) => d3.ascending(a.phage_name, b.phage_name)); if (mode === "all") return sorted; if (mode === "cluster") { return d3 .groups(sorted, (d) => d.cluster || "Unknown") .map(([, g]) => g[0]) .filter(Boolean); } return d3 .groups( sorted, (d) => d.cluster || "Unknown", (d) => d.subcluster && d.subcluster.trim() !== "" ? d.subcluster : "__NO_SUBCLUSTER__" ) .flatMap(([, subs]) => subs.map(([, g]) => g[0]).filter(Boolean)); } const wrap = html`

Cluster composition insights (all phages, all clusters)

`; const tableWrap = wrap.querySelector(".table-wrap"); let sortKey = "cluster"; let sortDir = "asc"; const data = d3 .groups(rows, (d) => d.cluster) .map(([cluster, phages]) => { const genera = new Set(phages.map((d) => d.host_genus).filter(Boolean)); const species = new Set( phages.map((d) => d.host_species).filter(Boolean) ); const strains = new Set(phages.map((d) => d.host_strain).filter(Boolean)); return { cluster, genusCount: genera.size, speciesCount: species.size, strainCount: strains.size, phages }; }); function sortRows(values) { return values.slice().sort((a, b) => { const result = sortKey === "cluster" ? d3.ascending(a.cluster, b.cluster) : d3.ascending(a[sortKey], b[sortKey]); return sortDir === "asc" ? result : -result; }); } function headerCell(label, key, width, align = "left") { const isActive = sortKey === key; const arrow = isActive ? (sortDir === "asc" ? " ▲" : " ▼") : ""; const th = html`${label}${arrow}`; th.onclick = () => { if (sortKey === key) { sortDir = sortDir === "asc" ? "desc" : "asc"; } else { sortKey = key; sortDir = "asc"; } render(); }; return th; } function render() { const sorted = sortRows(data); const table = html`

`; const headRow = table.querySelector("thead tr"); const tbody = table.querySelector("tbody"); headRow.append( headerCell("Cluster", "cluster", "160px"), headerCell("Genus count", "genusCount", "120px", "right"), headerCell("Species count", "speciesCount", "120px", "right"), headerCell("Strain count", "strainCount", "120px", "right"), html`Actions` ); for (const d of sorted) { const tr = html``; const actionCell = html``; const btn = html``; const status = html``; if (!user?.email || !user?.password) { btn.disabled = true; btn.style.background = "#f3f3f3"; btn.style.color = "#888"; btn.style.cursor = "not-allowed"; } else { btn.onmouseenter = () => (btn.style.background = "#f5f5f5"); btn.onmouseleave = () => (btn.style.background = "white"); btn.onclick = async () => { await downloadPhageSetAsFasta(pickPhages(d.phages, downloadMode), { button: btn, statusNode: status, filePrefix: `cluster_${d.cluster}`, headerMode: fastaHeaderMode }); }; } actionCell.append(btn, status); tr.append( html` ${d.cluster} `, html`${d.genusCount}`, html`${d.speciesCount}`, html`${d.strainCount}`, actionCell ); tbody.append(tr); } tableWrap.replaceChildren(table); } render(); return wrap; }3b:T53c,cacheStatusPanel = { const cacheCount = Object.keys(phameratorSequenceCache ?? {}).length; const wrap = html`

Phamerator Genomes Cached: ${cacheCount} cached sequences

`; const btn = wrap.querySelector(".clear-cache"); const status = wrap.querySelector(".status"); btn.onmouseenter = () => (btn.style.background = "#f5f5f5"); btn.onmouseleave = () => (btn.style.background = "white"); btn.onclick = () => { localStorage.removeItem(phameratorSequenceCacheKey); mutable phameratorSequenceCache = {}; status.textContent = "Clear Phamerator Cache."; }; return wrap; }3c:[] 2c:{"id":"4f41681c403da309","slug":"download-phage-genomes","title":"Download Genomes by Host or Cluster","thumbnail":"e5a2f5d75e5c1ad38223d736a646582df127e1f04d4b755d859e25d6009e4718","access_level":"public","create_time":"$D2026-04-17T17:44:22.117Z","update_time":"$D2026-08-11T14:19:35.812Z","view_time":null,"first_public_time":"$D2026-08-20T15:42:47.793Z","has_unpublished_edits":null,"fork":{"id":"9f8c8207fa24d7ed","slug":null,"title":"Download Genomes by Host or Cluster","owner":{"id":"d1dfc5f860fb8699","login":"phage","name":"WabushOnce"}},"stars":0,"starred":false,"owner":{"type":"team","id":"d1dfc5f860fb8699","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":"starter_2024"},"version":1007,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"3035ce62f81ebcd9","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":null}],"members":[{"type":"individual","id":"3035ce62f81ebcd9","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":null,"role":"editor"},{"type":"team","id":"d1dfc5f860fb8699","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":true,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"Download Genomes by Host or Cluster","cells":[{"id":0,"value":"# Download Genomes by Host or Cluster\n\n- Building a phylogeny with all phages is slow - this script can download one representative phage per cluster or subcluster\n- ---","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":494,"value":"### 1. Get Phage Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":941,"value":"#### Load Phages Genomes from Actinobacteriophages-All.fasta \n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":933,"value":"$2e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":841,"value":"viewof allGenomesFastaFile = Inputs.file({\n label: \"Back-up: Upload Actinobacteriophages-All.fasta\",\n accept: \".fasta,.fa,.fna,.txt\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":731,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":470,"value":"### 2. Filter Phages by Host or Cluster/Subcluster and Institution","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":45,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":186,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":239,"value":"#### Phages selected for FASTA","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":596,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":506,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":566,"value":"### 4. Download FASTA","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":391,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":741,"value":"---\n### Create a Phylogeny Tree \n- Browse to Observable Phylogeny Tree for steps to create a tree.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":4,"value":"---\n# Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":966,"value":"mtp0z569uy1he0jyq2njz0k032xc1z","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":995,"value":"downloadRowsFromResultsTable = {\n const selected = resultsTable?.selectedRows ?? [];\n return selected.length ? selected : filteredPhageRows;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":622,"value":"#### Option A (preferable): Use Phamerator - a more accurate method","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":272,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":332,"value":"$36","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","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 institutionOk =\n !selectedInstitutions.length ||\n selectedInstitutions.includes(d.institution_name);\n\n if (filterMode === \"host\") {\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 institutionOk && genusOk && speciesOk && strainOk;\n }\n\n const clusterOk =\n !selectedClusters.length || selectedClusters.includes(d.cluster);\n\n const subclusterOk =\n !selectedSubclusters.length || selectedSubclusters.includes(d.subcluster);\n\n return institutionOk && clusterOk && subclusterOk;\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":234,"value":"### Get Phamerator Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":970,"value":"","pinned":false,"hidden":false,"mode":"ojs","author":"$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":"$undefined"},{"id":361,"value":"mutable selectedGenera = []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":364,"value":"mutable selectedSpeciesList = []","pinned":false,"hidden":false,"mode":"ojs","author":"$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":"$undefined"},{"id":425,"value":"mutable selectedClusters = []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":427,"value":"mutable selectedSubclusters = []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":429,"value":"mutable selectedInstitutions = []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":439,"value":"mutable filterMode = \"host\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":534,"value":"pickPhagesForDownload = function (rows) {\n const sorted = (rows ?? [])\n .slice()\n .sort((a, b) => d3.ascending(a.phage_name, b.phage_name));\n\n if (downloadMode === \"all\") {\n return sorted;\n }\n\n if (downloadMode === \"cluster\") {\n return d3\n .groups(sorted, (d) => d.cluster || \"Unknown\")\n .map(([, group]) => group[0])\n .filter(Boolean);\n }\n\n return d3\n .groups(\n sorted,\n (d) => d.cluster || \"Unknown\",\n (d) =>\n d.subcluster && d.subcluster.trim() !== \"\"\n ? d.subcluster\n : \"__NO_SUBCLUSTER__\"\n )\n .flatMap(([, subgroups]) =>\n subgroups.map(([, group]) => group[0]).filter(Boolean)\n );\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":601,"value":"downloadMode = fastaDownloadPanel?.downloadMode ?? \"all\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":640,"value":"fastaHeaderMode = Generators.input(viewof fastaHeaderPanel).fastaHeaderMode","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":698,"value":"### Export Results Table to Excel","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":794,"value":"## DNA Sequence Back Up","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":837,"value":"import { Inputs } from \"@observablehq/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":844,"value":"allGenomesFastaText = allGenomesFastaFile\n ? await allGenomesFastaFile.text()\n : \"\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":847,"value":"function parseFasta(text) {\n if (!text || !text.trim()) return [];\n\n const lines = text.split(/\\r?\\n/);\n const records = [];\n let header = null;\n let seq = [];\n\n for (const line of lines) {\n if (!line.trim()) continue;\n\n if (line.startsWith(\">\")) {\n if (header) {\n records.push({\n header,\n sequence: seq.join(\"\").replace(/\\s+/g, \"\").toUpperCase()\n });\n }\n header = line.slice(1).trim();\n seq = [];\n } else {\n seq.push(line.trim());\n }\n }\n\n if (header) {\n records.push({\n header,\n sequence: seq.join(\"\").replace(/\\s+/g, \"\").toUpperCase()\n });\n }\n\n return records;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":849,"value":"function normalizePhageName(name) {\n return String(name || \"\")\n .trim()\n .toLowerCase()\n .replace(/[^a-z0-9]/g, \"\");\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":851,"value":"function extractCandidateNamesFromHeader(header) {\n const candidates = new Set();\n const h = header.trim();\n\n // Example:\n // \"Mycobacterium phage 20ES complete sequence, 53124 bp ...\"\n const m1 = h.match(/\\bphage\\s+([A-Za-z0-9._-]+)\\b/i);\n if (m1) candidates.add(m1[1]);\n\n // First token after \"phage\"\n const m2 = h.match(/\\bphage\\s+([^,;]+)/i);\n if (m2) {\n const token = m2[1].trim().split(/\\s+/)[0];\n if (token) candidates.add(token);\n }\n\n // Also add first comma-delimited fragment’s last token as a fallback\n const firstChunk = h.split(\",\")[0];\n const words = firstChunk.trim().split(/\\s+/);\n if (words.length) candidates.add(words[words.length - 1]);\n\n return [...candidates];\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":853,"value":"allGenomeRecords = parseFasta(allGenomesFastaText)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":855,"value":"allGenomeIndex = {\n const exact = new Map();\n const contains = [];\n\n for (const rec of allGenomeRecords) {\n const candidates = extractCandidateNamesFromHeader(rec.header);\n\n for (const candidate of candidates) {\n const key = normalizePhageName(candidate);\n if (key && !exact.has(key)) exact.set(key, rec);\n }\n\n contains.push({\n ...rec,\n normalizedHeader: normalizePhageName(rec.header)\n });\n }\n\n return { exact, contains };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":857,"value":"function findGenomeForPhage(phageName, genomeIndex) {\n const key = normalizePhageName(phageName);\n if (!key) return null;\n\n // 1) exact candidate-name match\n if (genomeIndex.exact.has(key)) {\n return {\n matchType: \"exact\",\n record: genomeIndex.exact.get(key)\n };\n }\n\n // 2) header contains normalized phage name\n const contained = genomeIndex.contains.find(d => d.normalizedHeader.includes(key));\n if (contained) {\n return {\n matchType: \"header-contains\",\n record: contained\n };\n }\n\n return null;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":911,"value":"pickPhages = function (rows, mode) {\n const sorted = (rows ?? [])\n .slice()\n .sort((a, b) => d3.ascending(a.phage_name, b.phage_name));\n\n if (mode === \"all\") return sorted;\n\n if (mode === \"cluster\") {\n return d3\n .groups(sorted, (d) => d.cluster || \"Unknown\")\n .map(([, group]) => group[0])\n .filter(Boolean);\n }\n\n return d3\n .groups(\n sorted,\n (d) => d.cluster || \"Unknown\",\n (d) =>\n d.subcluster && d.subcluster.trim() !== \"\"\n ? d.subcluster\n : \"__NO_SUBCLUSTER__\"\n )\n .flatMap(([, subs]) => subs.map(([, group]) => group[0]).filter(Boolean));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":918,"value":"filteredPhageRows = {\n const rows = selectedRows ?? [];\n return pickPhages(rows, downloadMode);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":859,"value":"phageNamesFromResults = Array.from(\n new Set(\n pickPhages(selectedRows ?? [], fastaDownloadPanel?.downloadMode ?? \"all\")\n .map((d) => d.phage_name)\n .filter(Boolean)\n )\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":863,"value":"backupPhageSequences = {\n if (!allGenomeRecords.length) {\n return {\n found: [],\n missing: phageNamesFromResults,\n sequenceByPhage: new Map()\n };\n }\n\n const found = [];\n const missing = [];\n const sequenceByPhage = new Map();\n\n for (const phageName of phageNamesFromResults) {\n const hit = findGenomeForPhage(phageName, allGenomeIndex);\n\n if (hit?.record?.sequence) {\n const item = {\n phage: phageName,\n sequence: hit.record.sequence,\n header: hit.record.header,\n matchType: hit.matchType,\n length: hit.record.sequence.length\n };\n found.push(item);\n sequenceByPhage.set(phageName, item);\n } else {\n missing.push(phageName);\n }\n }\n\n return { found, missing, sequenceByPhage };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":865,"value":"Inputs.table(\n backupPhageSequences.found.map(d => ({\n phage: d.phage,\n length: d.length,\n matchType: d.matchType,\n header: d.header\n })),\n {label: \"Phages found in uploaded multifasta\"}\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":867,"value":"viewof missingPhagePicker = Inputs.select(\n backupPhageSequences.missing,\n {\n label: \"Select a phage missing from the multifasta\",\n value: backupPhageSequences.missing[0]\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":869,"value":"viewof missingPhageFastaFile = Inputs.file({\n label: \"Upload FASTA for selected missing phage\",\n accept: \".fasta,.fa,.fna,.txt\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":871,"value":"missingPhageFastaText = missingPhageFastaFile ? await missingPhageFastaFile.text() : \"\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":873,"value":"manualMissingPhageRecord = {\n const recs = parseFasta(missingPhageFastaText);\n if (!recs.length || !missingPhagePicker) return null;\n\n // Prefer a header that contains the selected phage name\n const key = normalizePhageName(missingPhagePicker);\n const preferred =\n recs.find((r) => normalizePhageName(r.header).includes(key)) || recs[0];\n\n return {\n phage: missingPhagePicker,\n sequence: preferred.sequence,\n header: preferred.header,\n length: preferred.sequence.length,\n source: \"manual-upload\"\n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":878,"value":"allResolvedPhageSequences = {\n const map = new Map(backupPhageSequences.sequenceByPhage);\n\n if (manualMissingPhageRecord?.sequence) {\n map.set(manualMissingPhageRecord.phage, manualMissingPhageRecord);\n }\n\n return map;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":882,"value":"resolvedSequenceArray = Array.from(allResolvedPhageSequences.values()).map(d => ({\n phage: d.phage,\n length: d.length,\n source: d.source ?? \"multifasta\",\n header: d.header\n}))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":884,"value":"Inputs.table(resolvedSequenceArray, {\n label: \"Resolved phage DNA sequences\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":886,"value":"unresolvedAfterManualUpload = phageNamesFromResults.filter(\n name => !allResolvedPhageSequences.has(name)\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":888,"value":"Inputs.table(\n unresolvedAfterManualUpload.map(phage => ({ phage })),\n { label: \"Still unresolved phages\" }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":547,"value":"---\n# Clusters with more than one host.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":509,"value":"$3a","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":538,"value":"$3b","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W3c","stdlib":"1","titling":"auto"}} 2d:"$2c:body"