Phage Gene Analysis

28:null 29:["$","title",null,{"children":"Pharmonizer (Phage Harmonization) | WabushOnce | Observable"}] 2e:T438, ### Genome Annotation Tools 1. Spreadsheet to track gene verification 2. Identify Phams with multiple functions 3. Lists ORFS in gaps to be checked for potential genes 4. Identify Pham genes with large protein length differences 5. Highlight common overlaps/gaps, functions, or gene lengths in Phams ### Tools to download Phamerator data: 1. DNA sequences in a Cluster (.fasta) 2. DNA/Protein sequence in a Pham (.fasta) - option to filer by cluster 4. DNA sequences upstream of genes in a Pham - option to filter by cluster ### Cluster annotation tips: - SEAPHAGE'S cluster specific annotation tips - Functional assignment list ### Suggestions and improvements: - We are happy to improve the user experience and add features. Please send suggestions to Kieran Furlong (kfurl048 at uOttawa.ca) ---2f:T1e63,viewof phageTransferUI = { // Create the container for the listboxes and buttons let container = html`

Cluster phages (0)

Phages to Harmonize (0)

`; // Function to update counts function updateCounts(prefix) { const clusterCount = container.querySelector(`#clusterCount${prefix}`); const selectedCount = container.querySelector(`#selectedCount${prefix}`); const clusterPhages = container.querySelector(`#clusterPhages${prefix}`); const selectedPhages = container.querySelector(`#selectedPhages${prefix}`); clusterCount.textContent = clusterPhages.options.length; selectedCount.textContent = selectedPhages.options.length; } // Add functionality to the first set of listboxes function addFunctionality(prefix) { let clusterPhages = container.querySelector(`#clusterPhages${prefix}`); let selectedPhages = container.querySelector(`#selectedPhages${prefix}`); let addAllButton = container.querySelector(`#addAll${prefix}`); let removeAllButton = container.querySelector(`#removeAll${prefix}`); let addSelectedButton = container.querySelector(`#addSelected${prefix}`); let removeSelectedButton = container.querySelector( `#removeSelected${prefix}` ); let addDraftButton = container.querySelector(`#addDraft${prefix}`); let removeDraftButton = container.querySelector(`#removeDraft${prefix}`); let addAnnotatedButton = container.querySelector(`#addAnnotated${prefix}`); let removeAnnotatedButton = container.querySelector( `#removeAnnotated${prefix}` ); // Add functionality for double-click to move items clusterPhages.ondblclick = () => { Array.from(clusterPhages.selectedOptions).forEach((option) => { selectedPhages.add(new Option(option.text, option.value)); option.remove(); }); updateCounts(prefix); }; selectedPhages.ondblclick = () => { Array.from(selectedPhages.selectedOptions).forEach((option) => { clusterPhages.add(new Option(option.text, option.value)); option.remove(); }); let sortedOptions = Array.from(clusterPhages.options).sort((a, b) => a.value.localeCompare(b.value) ); clusterPhages.innerHTML = ""; sortedOptions.forEach((option) => clusterPhages.appendChild(option)); updateCounts(prefix); }; // Add functionality for "Add all >>" button addAllButton.onclick = () => { Array.from(clusterPhages.options).forEach((option) => { selectedPhages.add(new Option(option.text, option.value)); }); clusterPhages.innerHTML = ""; updateCounts(prefix); }; // Add functionality for "<< Remove all" button removeAllButton.onclick = () => { Array.from(selectedPhages.options).forEach((option) => { clusterPhages.add(new Option(option.text, option.value)); }); selectedPhages.innerHTML = ""; let sortedOptions = Array.from(clusterPhages.options).sort((a, b) => a.value.localeCompare(b.value) ); clusterPhages.innerHTML = ""; sortedOptions.forEach((option) => clusterPhages.appendChild(option)); updateCounts(prefix); }; // Add functionality for "Add >" button addSelectedButton.onclick = () => { Array.from(clusterPhages.selectedOptions).forEach((option) => { selectedPhages.add(new Option(option.text, option.value)); option.remove(); }); updateCounts(prefix); }; // Add functionality for "< Remove" button removeSelectedButton.onclick = () => { Array.from(selectedPhages.selectedOptions).forEach((option) => { clusterPhages.add(new Option(option.text, option.value)); option.remove(); }); let sortedOptions = Array.from(clusterPhages.options).sort((a, b) => a.value.localeCompare(b.value) ); clusterPhages.innerHTML = ""; sortedOptions.forEach((option) => clusterPhages.appendChild(option)); updateCounts(prefix); }; // Add functionality for "Draft >" button addDraftButton.onclick = () => { Array.from(clusterPhages.options) .filter((option) => option.text.endsWith("_Draft")) .forEach((option) => { selectedPhages.add(new Option(option.text, option.value)); option.remove(); }); updateCounts(prefix); }; // Add functionality for "< Draft" button removeDraftButton.onclick = () => { Array.from(selectedPhages.options) .filter((option) => option.text.endsWith("_Draft")) .forEach((option) => { clusterPhages.add(new Option(option.text, option.value)); option.remove(); }); let sortedOptions = Array.from(clusterPhages.options).sort((a, b) => a.value.localeCompare(b.value) ); clusterPhages.innerHTML = ""; sortedOptions.forEach((option) => clusterPhages.appendChild(option)); updateCounts(prefix); }; // Add functionality for "Annotated >" button addAnnotatedButton.onclick = () => { Array.from(clusterPhages.options) .filter((option) => !option.text.endsWith("_Draft")) .forEach((option) => { selectedPhages.add(new Option(option.text, option.value)); option.remove(); }); updateCounts(prefix); }; // Add functionality for "< Annotated" button removeAnnotatedButton.onclick = () => { Array.from(selectedPhages.options) .filter((option) => !option.text.endsWith("_Draft")) .forEach((option) => { clusterPhages.add(new Option(option.text, option.value)); option.remove(); }); let sortedOptions = Array.from(clusterPhages.options).sort((a, b) => a.value.localeCompare(b.value) ); clusterPhages.innerHTML = ""; sortedOptions.forEach((option) => clusterPhages.appendChild(option)); updateCounts(prefix); }; } // Apply functionality to the first set of listboxes addFunctionality("1"); updateCounts("1"); return container; }30:T4b8,phamFunctionsTable = Inputs.table( determineDataSource().map((item) => { const newRow = processItem(item); // Convert Pham to a number if it contains numeric values newRow.Pham = parseInt(newRow.Pham, 10) || newRow.Pham; // keeps it as a string if it’s non-numeric // Add Gene only if filterPhamsWithDifferentFunctions is not "All phages" if (filterPhamsWithDifferentFunctions !== "All phages") { newRow.Gene = parseInt(newRow.Gene, 10) || newRow.Gene; // keeps it as a string if it’s non-numeric return { Gene: newRow["Gene"], ...newRow }; // Keep Gene as second column } else { return { Pham: newRow.Pham, ...newRow }; // Exclude Gene column } }), { format: { Pham: (phamName) => htl.html`

${phamName}

`, Gene: (geneName) => geneName ? htl.html`

${filterPhamsWithDifferentFunctions}_${geneName}

` : "" }, layout: "auto", rows: 15 } )31:T76c,showGapSequence = Inputs.table(parseGapSequences, { sort: "Gene", format: { Upstream_Gene: (Gene, row) => htl.html`${Gene}`, DNA: (DNA, row) => showFullSequences === "Yes" ? htl.html`${DNA}` : htl.html`DNA`, Protein: (Protein, row) => showFullSequences === "Yes" ? htl.html`${Protein}` : htl.html`Protein`, GeneMarkS: (GeneMarkS, row) => { // Extract the page number from the GeneMarkS URL const pageMatch = GeneMarkS.match(/page=(\d+)/); const pageNumber = pageMatch ? pageMatch[1] : "unknown"; // Use 'unknown' if no match found return htl.html`GeneMarkS (p.${pageNumber})`; }, GeneMarkHost: (GeneMarkHost, row) => { // Extract the page number from the GeneMark Host URL const pageMatch = GeneMarkHost.match(/page=(\d+)/); const pageNumber = pageMatch ? pageMatch[1] : "unknown"; // Use 'unknown' if no match found return htl.html`GeneMark (p.${pageNumber})`; } }, columns: [ "Upstream_Gene", "ORF_bp", "DNA_Strand", "Start_bp", "Start_Codon", "Stop_bp", "Stop_Codon", "GeneMarkS", "GeneMarkHost", "Frame", "DNA", "Protein" ], layout: "auto", rows: 15 })32:T469,// Gene function analysis table geneFunctionAnalysisResults = { const filteredData = showPhamFunctions === "Different functions" ? analyzeFunctions.filter((d) => d.PercentCalled !== "100.00%") : analyzeFunctions.filter((d) => d.PercentCalled === "100.00%"); // If no data, return an empty array if (filteredData.length === 0) { console.log("No phams to display."); return []; } // Get the length dynamically for table columns const length = Object.keys(filteredData[0]).length; // Return the table return Inputs.table(filteredData, { format: { Pham: (pham) => htl.html`${pham}`, ...Array.from({ length }, (_, i) => i).reduce((acc, idx) => { const geneKey = `NonCommonGeneFunctionGene${idx + 1}`; const gapKey = `GeneFunction${idx + 1}`; acc[geneKey] = (gene) => gene ? htl.html`${gene}` : ""; return acc; }, {}) }, layout: "auto", rows: 20 }); }33:T43b,geneLengthAnalysisResults = { const filteredData = showPhamLengths === "Different lengths" ? analyzeLengths.filter((d) => d.PercentCalled !== "100.00%") : analyzeLengths.filter((d) => d.PercentCalled === "100.00%"); // If no data, return an empty array if (filteredData.length === 0) { console.log("No phams to display."); return []; } // Get the length dynamically for table columns const length = Object.keys(filteredData[0]).length; // Return the table return Inputs.table(filteredData, { format: { Pham: (pham) => htl.html`${pham}`, ...Array.from({ length }, (_, i) => i).reduce((acc, idx) => { const geneKey = `NonCommonGeneLengthGene${idx + 1}`; const gapKey = `GeneLength${idx + 1}`; acc[geneKey] = (gene) => gene ? htl.html`${gene}` : ""; return acc; }, {}) }, layout: "auto", rows: 15 }); }34:T8a3,{ const progressContainer = html`

`; async function downloadFasta() { console.log("Starting download..."); const progressBar = progressContainer.querySelector("#progressBar"); progressBar.style.width = "0%"; // Reset progress bar to 0% at the start of the download let allFastaData = ""; const phages = phagesByCluster_ClusterDNASequenceDownloads; // Make sure this is correctly populated let index = 0; for (const phage of phages) { console.log(`Fetching data for ${phage.phagename}`); let genomeData = await getPhameratorData( dataset, `/genome/${phage.phagename}/`, user.email, user.password ); if (genomeData && genomeData.sequence) { allFastaData += `>${phage.phagename}\n${genomeData.sequence}\n`; console.log(`Data fetched for ${phage.phagename}`); } const progressPercent = ((index + 1) / phages.length) * 100; progressBar.style.width = `${progressPercent}%`; console.log(`Progress: ${progressPercent}%`); await new Promise((resolve) => setTimeout(resolve, 100)); // Just for demonstration, can be removed index++; } const blob = new Blob([allFastaData], { type: "text/plain" }); const href = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = href; link.download = `${dataset}_${selectedDataCluster}_Cluster_DNA.fasta`; document.body.appendChild(link); link.click(); document.body.removeChild(link); URL.revokeObjectURL(href); console.log("Download completed."); } return html`

${Inputs.button(`Download Cluster "${selectedDataCluster}" Sequences`, { async reduce() { console.log("Button clicked."); progressContainer.style.display = "block"; await downloadFasta(); progressContainer.style.display = "none"; } })} ${progressContainer}

`; }35:T6b2,{ const button = Inputs.button( `Download Pham "${selectedDataPham}" DNA Sequences`, { async reduce() { const progressBar = document.getElementById("progressBar"); const phamData = phamData_IncludingOnlyPhagesFromSelectedCluster; // Ensure this data is accessible let allFastaData = ""; for (let i = 0; i < phamData.length; i++) { const entry = phamData[i]; allFastaData += `>${entry.phageID}_${entry.name}\n${entry.sequence}\n`; // Update the progress bar const progressPercent = ((i + 1) / phamData.length) * 100; progressBar.style.width = `${progressPercent}%`; await new Promise((resolve) => setTimeout(resolve, 10)); // Simulate a short delay for UI updates } // Create and trigger the download const blob = new Blob([allFastaData], { type: "text/plain" }); const fileName = `${selectedDataset}_${selectedDataPham}_DNA_Sequences.fasta`; const href = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = href; link.download = fileName; document.body.appendChild(link); link.click(); document.body.removeChild(link); URL.revokeObjectURL(href); progressBar.style.width = "0%"; // Reset the progress bar } } ); const progressContainer = html`

`; return html`

${button} ${progressContainer}

`; }36:T7b0,{ const button = Inputs.button( `Download Pham "${selectedDataPham}" Protein Sequences`, { async reduce() { const progressBar = document.getElementById("progressBar"); const phamData = filterPhamDownloadData === "All pham genes" ? phamily : phamData_IncludingOnlyPhagesFromSelectedCluster; const fastaEntries = []; // Use an array to collect entries for (let i = 0; i < phamData.length; i++) { const entry = phamData[i]; fastaEntries.push( `>${entry.phageID}_${entry.name}\n${entry.translation}\n` ); // Update the progress bar less frequently, only on certain iterations if (i % 10 === 0 || i === phamData.length - 1) { const progressPercent = ((i + 1) / phamData.length) * 100; progressBar.style.width = `${progressPercent}%`; } } // Combine all fasta entries into a single string const allFastaData = fastaEntries.join(""); // Create and trigger the download const blob = new Blob([allFastaData], { type: "text/plain" }); const fileName = `${selectedDataset}_${selectedDataPham}_Protein_Sequences.fasta`; const href = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = href; link.download = fileName; document.body.appendChild(link); link.click(); document.body.removeChild(link); URL.revokeObjectURL(href); progressBar.style.width = "0%"; // Reset the progress bar } } ); const progressContainer = html`

`; return html`

${button} ${progressContainer}

`; }37:T49c,phamsWithDifferentFunctionsByCluster = { // The data "genesbycluster" contains the clusters' genes const groupedByPhamName = phageGenesToHarmonize.reduce((accumulator, gene) => { const phamName = gene.phamName; const geneFunction = gene.genefunction || "hypothetical protein"; // Initialize phamName and geneFunction group if not exist if (!accumulator.has(phamName)) { accumulator.set(phamName, new Map()); } if (!accumulator.get(phamName).has(geneFunction)) { accumulator.get(phamName).set(geneFunction, []); } accumulator.get(phamName).get(geneFunction).push({ phageID: gene.phageID, name: gene.name }); return accumulator; }, new Map()); // Filter phamName entries to include only those with more than one distinct function const result = []; for (const [phamName, functions] of groupedByPhamName.entries()) { const details = []; for (const [geneFunction, genes] of functions.entries()) { details.push({ geneFunction, genes }); } if (details.length > 1) { // Ensuring there are multiple functions result.push({ phamName, details }); } } return result; }38:T585,phamsWithDifferentFunctionsByAnnotatedPhages = { // Step 1: Group data by phamName const groupedByPhamName = annotatedPhageGenesByCluster.reduce( (accumulator, gene) => { const phamName = gene.phamName; const geneFunction = gene.genefunction || "hypothetical protein"; if (!accumulator[phamName]) { accumulator[phamName] = {}; } if (!accumulator[phamName][geneFunction]) { accumulator[phamName][geneFunction] = []; } // Only add gene data if phageID is not in draftPhageNames if (!draftPhagesByCluster.has(gene.phageID)) { accumulator[phamName][geneFunction].push({ phageID: gene.phageID, name: gene.name }); } return accumulator; }, {} ); // Step 2: Filter phamName entries to include only those with more than one gene function const result = []; Object.keys(groupedByPhamName).forEach((phamName) => { const functions = groupedByPhamName[phamName]; const phamData = { phamName: phamName, details: [] }; Object.keys(functions).forEach((geneFunction) => { if (functions[geneFunction].length > 0) { phamData.details.push({ geneFunction: geneFunction, genes: functions[geneFunction] }); } }); if (phamData.details.length > 1) { result.push(phamData); } }); return result; }39:T5a9,function processItem(item) { const newRow = { Pham: item.phamName }; let applyFunction; if ( showPhages === "Functions Only" && filterPhamsWithDifferentFunctions !== "All phages" ) { applyFunction = (detail) => formatFunctionWithFilteredPhages(detail); } else if (showPhages === "Functions and Phages") { applyFunction = (detail) => formatFunctionWithAllPhages(detail); } else { applyFunction = (detail) => detail.geneFunction; } for (let index = 0; index < item.details.length; index++) { const detail = item.details[index]; const key = `Function ${index + 1}`; newRow[key] = applyFunction(detail); } // Store only `Gene` name as a string for consistent sorting if (filterPhamsWithDifferentFunctions !== "All phages") { const specificPhageDetail = item.details.find((detail) => detail.genes.some( (gene) => gene.phageID.trim() === filterPhamsWithDifferentFunctions ) ); if (specificPhageDetail) { const specificPhage = specificPhageDetail.genes.find( (gene) => gene.phageID.trim() === filterPhamsWithDifferentFunctions ); if (specificPhage) { newRow["Gene"] = specificPhage.name; // Store only the name as a simple string } } } // Convert Pham to a number if it contains numeric values newRow.Pham = parseInt(newRow.Pham, 10) || newRow.Pham; // keeps it as a string if it’s non-numeric return newRow; }3a:T1a3f,getPhageGeneAndGapSequences = { // Get all the phage data in the cluster let phageDataArray = await fetchAllPhageData( phageGenesToHarmonize_UniquePhages_DraftNaming, dataset, apiKey ); let GenesGroupedByPham = {}; //----------------------------------------------------------------- // Iterate each phage that is selected for harmonization //----------------------------------------------------------------- phageDataArray.forEach((genomeData, index) => { if (!genomeData || !genomeData.sequence) return; const phage = phageGenesToHarmonize_UniquePhages_DraftNaming[index]; //----------------------------------------------------------------- // Iterate each gene in the phage //----------------------------------------------------------------- genomeData.genes.forEach((gene, j) => { const prevGene = genomeData.genes[j - 1]; const nextGene = genomeData.genes[j + 1] || {}; //--------------------------------------------- // Calculate the gap start position //--------------------------------------------- const gapStart = gene.name != "1" ? gene.direction === "forward" ? (prevGene?.direction === "reverse" ? prevGene.start : prevGene?.stop) + 1 : prevGene?.direction === "reverse" ? prevGene.start : prevGene?.stop : 2; //--------------------------------------------- // Calculate the gap stop position //--------------------------------------------- const gapStop = gene.direction === "forward" ? gene.start - 1 : gene.stop - 1; //----------------------------------------------------------------- // Get the gap DNA sequence & complementary strand sequence //----------------------------------------------------------------- let topStrandGapSequence = ""; let bottomStrandGapSequence = ""; if (gene.direction === "forward") { topStrandGapSequence = genomeData.sequence.substring( gapStart - 1, gapStop ); bottomStrandGapSequence = reverseString( complementarySequence( genomeData.sequence.substring(gapStart - 1, gapStop) ) ); } else { bottomStrandGapSequence = reverseString( complementarySequence( genomeData.sequence.substring(gapStart, gapStop) ) ); topStrandGapSequence = genomeData.sequence.substring(gapStart, gapStop); } let geneSequence = gene.direction === "forward" ? genomeData.sequence.substring(gene.start - 1, gene.stop) : reverseString( complementarySequence( genomeData.sequence.substring(gene.start, gene.stop - 1) ) ); //----------------------------------------------------------------- // Get the previous gene's DNA sequence and direction //----------------------------------------------------------------- let previousGeneSequence = ""; let previousGeneDirection = ""; if (prevGene) { previousGeneSequence = prevGene.direction === "forward" ? genomeData.sequence.substring(prevGene.start - 1, prevGene.stop) : reverseString( complementarySequence( genomeData.sequence.substring( prevGene.start, prevGene.stop - 1 ) ) ); previousGeneDirection = prevGene.direction; } //----------------------------------------------------------------- // Get the next gene's DNA sequence //----------------------------------------------------------------- let nextGeneSequence = ""; let nextGeneDirection = nextGene.direction; if (nextGeneDirection) { nextGeneSequence = nextGeneDirection === "forward" ? genomeData.sequence.substring(nextGene.start - 1, nextGene.stop) : reverseString( complementarySequence( genomeData.sequence.substring( nextGene.start, nextGene.stop - 1 ) ) ); } //----------------------------------------------------------------- // Add gene information to the result //----------------------------------------------------------------- let geneInfo = { phagename: phage.phagename, name: gene.name, pham: gene.phamName, direction: gene.direction, gap: gene.gap, geneStart: gene.start, geneStop: gene.stop, geneSequence, previousGeneSequence, previousGeneDirection, nextGeneSequence, nextGeneDirection, gapStart, gapStop, topStrandGapSequence, bottomStrandGapSequence }; GenesGroupedByPham[gene.phamName] = GenesGroupedByPham[gene.phamName] || { genes: [], geneFunction: gene.genefunction || "Unknown" }; GenesGroupedByPham[gene.phamName].genes.push(geneInfo); }); //----------------------------------------------------------------- // Handle last gene to the end of the genome //----------------------------------------------------------------- if (genomeData.genes.length > 0) { const lastGene = genomeData.genes[genomeData.genes.length - 1]; let endGapSequence = ""; let gapStart = lastGene.direction === "forward" ? lastGene.stop : lastGene.start - 1; if (lastGene.direction === "forward") { endGapSequence = genomeData.sequence.substring( lastGene.stop, genomeData.sequence.length ); } else { endGapSequence = genomeData.sequence.substring( lastGene.start - 1, genomeData.sequence.length ); } const bottomStrandGapSequence = reverseString( complementarySequence(endGapSequence) ); let endGeneInfo = { phagename: phage.phagename, name: `${lastGene.name}_ToGenomeEnd`, direction: lastGene.direction, gapStart: gapStart, gapStop: genomeData.sequence.length, topStrandGapSequence: endGapSequence, bottomStrandGapSequence }; GenesGroupedByPham[`${lastGene.name}_ToGenomeEnd`] = GenesGroupedByPham[ `${lastGene.name}_ToGenomeEnd` ] || { genes: [] }; GenesGroupedByPham[`${lastGene.name}_ToGenomeEnd`].genes.push( endGeneInfo ); } }); return GenesGroupedByPham; }3b:T1c2a,findGenesInGapSequences = { const gapArray = []; const startCodonList = ["ATG", "TTG", "GTG"]; const stopCodonList = ["TAA", "TAG", "TGA"]; for (const phageId in getPhageGeneAndGapSequencesFilteredByORF) { const phageData = getPhageGeneAndGapSequencesFilteredByORF[phageId]; phageData.genes.forEach((gene) => { let nextGeneOverlapSequenceTopStrand = ""; let nextGeneOverlapSequenceBottomStrand = ""; let previousGeneOverlapSequenceTopStrand = ""; let previousGeneOverlapSequenceBottomStrand = ""; const previousGeneSequence = gene.previousGeneSequence || ""; const currentGeneSequence = gene.geneSequence || ""; let topStrandGapSequence = gene.topStrandGapSequence || ""; let bottomStrandGapSequence = gene.bottomStrandGapSequence || ""; if (gene.direction === "forward") { nextGeneOverlapSequenceTopStrand = nextGeneOverlap > 0 ? currentGeneSequence.slice(0, nextGeneOverlap) : ""; nextGeneOverlapSequenceBottomStrand = reverseString( complementarySequence(nextGeneOverlapSequenceTopStrand) ); if (gene.previousGeneDirection === "forward") { previousGeneOverlapSequenceTopStrand = previousGeneOverlap > 0 ? previousGeneSequence.slice(-previousGeneOverlap) : ""; previousGeneOverlapSequenceBottomStrand = reverseString( complementarySequence(previousGeneOverlapSequenceTopStrand) ); } else { previousGeneOverlapSequenceBottomStrand = previousGeneOverlap > 0 ? previousGeneSequence.slice(0, previousGeneOverlap) : ""; previousGeneOverlapSequenceTopStrand = reverseString( complementarySequence(previousGeneOverlapSequenceBottomStrand) ); } } else { nextGeneOverlapSequenceBottomStrand = nextGeneOverlap > 0 ? currentGeneSequence.slice(-nextGeneOverlap) : ""; nextGeneOverlapSequenceTopStrand = reverseString( complementarySequence(nextGeneOverlapSequenceBottomStrand) ); if (gene.previousGeneDirection === "forward") { previousGeneOverlapSequenceTopStrand = previousGeneOverlap > 0 ? previousGeneSequence.slice(-previousGeneOverlap) : ""; previousGeneOverlapSequenceBottomStrand = reverseString( complementarySequence(previousGeneOverlapSequenceTopStrand) ); } else { previousGeneOverlapSequenceBottomStrand = previousGeneOverlap > 0 ? previousGeneSequence.slice(0, previousGeneOverlap) : ""; previousGeneOverlapSequenceTopStrand = reverseString( complementarySequence(previousGeneOverlapSequenceBottomStrand) ); } } const topStrandStopSiteSearchSequence = previousGeneOverlapSequenceTopStrand + topStrandGapSequence + nextGeneOverlapSequenceTopStrand; const bottomStrandStopSiteSearchSequence = nextGeneOverlapSequenceBottomStrand + bottomStrandGapSequence + previousGeneOverlapSequenceBottomStrand; const stopCodonsTopStrand = []; const gapStart = gene.gapStart; const gapStop = gene.gapStop; for (let i = 0; i < topStrandStopSiteSearchSequence.length - 2; i++) { const codon = topStrandStopSiteSearchSequence.substr(i, 3); if (stopCodonList.includes(codon)) { const stopCodon = { stopCodon: codon, stopCodonBP: gene.previousGeneSequence ? gapStart + i - previousGeneOverlap : gapStart + i, stopCodonPosition: i, geneStrand: "FORWARD", startCodons: [] }; for (let j = i - 3; j >= 0; j -= 3) { const startCodon = topStrandStopSiteSearchSequence.substr(j, 3); if (stopCodonList.includes(startCodon)) break; if (startCodonList.includes(startCodon)) { stopCodon.startCodons.push({ gapStart, startCodon, newGeneStart: gene.previousGeneSequence ? gapStart + j - previousGeneOverlap : gapStart + j, ORF: i - j + 3, gapDNASequence: topStrandStopSiteSearchSequence.substring( j, i + 3 ), gapProteinSequence: dnaToProtein( topStrandStopSiteSearchSequence.substring(j, i + 3) ) }); } } stopCodonsTopStrand.push(stopCodon); } } const stopCodonsBottomStrand = []; for (let i = 0; i < bottomStrandStopSiteSearchSequence.length - 2; i++) { const codon = bottomStrandStopSiteSearchSequence.substr(i, 3); if (stopCodonList.includes(codon)) { const stopCodonPosition = i; const stopCodonBP = gapStop + nextGeneOverlap - stopCodonPosition; const stopCodon = { stopCodon: codon, stopCodonBP, //stopCodonBP: gene.nextGeneSequence // ? gapStop + nextGeneOverlap - stopCodonPosition // : gapStop + nextGeneOverlap - stopCodonPosition, stopCodonPosition: i, geneStrand: "reverse", startCodons: [] }; for (let j = i - 3; j >= 0; j -= 3) { const startCodon = bottomStrandStopSiteSearchSequence.substr(j, 3); if (stopCodonList.includes(startCodon)) break; if (startCodonList.includes(startCodon)) { const gapDNASequence = bottomStrandStopSiteSearchSequence.substring(j, i + 3); const newGeneStart = gapStop + nextGeneOverlap - j; stopCodon.startCodons.push({ startCodon, newGeneStart, ORF: newGeneStart - stopCodonBP, gapDNASequence, gapProteinSequence: dnaToProtein(gapDNASequence) }); } } stopCodonsBottomStrand.push(stopCodon); } } gapArray.push({ phagename: gene.phagename, name: gene.name, gap: gene.gap, direction: gene.direction, sequence: currentGeneSequence, previousGeneSequence, nextGeneSequence: gene.nextGeneSequence, gapStart, gapStop, topStrandGapSequence, bottomStrandGapSequence, nextGeneOverlapSequenceTopStrand, nextGeneOverlapSequenceBottomStrand, previousGeneOverlapSequenceTopStrand, previousGeneOverlapSequenceBottomStrand, topStrandStopSiteSearchSequence, bottomStrandStopSiteSearchSequence, stopCodonsTopStrand, stopCodonsBottomStrand }); }); } gapArray.sort((a, b) => { const phageComparison = a.phagename.localeCompare(b.phagename); if (phageComparison !== 0) return phageComparison; return parseInt(a.name) - parseInt(b.name); }); return gapArray; }3c:Tbed,parseGapSequences = { const result = []; for (const item of filteredData) { const cleanedPhagename = item.phagename?.replace("_Draft", "") || "Unknown"; // Handle GenomeEnd separately (no strands or stopCodons to process) if (item.name === "GenomeEnd") { result.push({ Upstream_Gene: `${cleanedPhagename}_CDS_${item.name}`, Gene: item.name, DNA_Strand: "N/A", ORF_bp: "N/A", Start_Codon: "N/A", Start_bp: item.newGeneStart || "N/A", Stop_Codon: "N/A", Stop_bp: item.geneStop || "N/A", GeneMarkS: `https://phagesdb.org/genemarks/${cleanedPhagename}`, GeneMarkHost: `https://phagesdb.org/genemarkhost/${cleanedPhagename}/5/`, Page: "N/A", DNA: item.geneSequence || "", Protein: "N/A" // No protein sequence for GenomeEnd }); continue; } const strands = ["stopCodonsBottomStrand", "stopCodonsTopStrand"]; for (const strand of strands) { if (!item[strand]) continue; // Skip if strand is undefined for (const stopCodon of item[strand]) { if (!stopCodon.startCodons) continue; // Skip if startCodons is undefined for (const startCodon of stopCodon.startCodons) { if ( selectORFLength === "All" || startCodon.ORF > selectORFLength - 1 ) { const page = 2 + Math.floor((startCodon.newGeneStart - 1) / 2125); //Calculate the frame of the ORF based on the startCodon position const pre_frame = Math.floor((startCodon.newGeneStart / 3) * 10) % 10; const DNA_Strand = stopCodon.geneStrand; let Frame = "N/A"; // Calculate the frame of the potential gene if (DNA_Strand === "FORWARD") { if (pre_frame === 3) Frame = "1st"; else if (pre_frame === 6) Frame = "2nd"; else if (pre_frame === 0) Frame = "3rd"; } else if (strand === "stopCodonsBottomStrand") { if (pre_frame === 3) Frame = "4th"; else if (pre_frame === 6) Frame = "5th"; else if (pre_frame === 0) Frame = "6th"; } result.push({ Upstream_Gene: `${cleanedPhagename}_CDS_${item.name}`, Gene: item.name, DNA_Strand, ORF_bp: startCodon.ORF || "N/A", Start_Codon: startCodon.startCodon || "N/A", Start_bp: startCodon.newGeneStart || "N/A", Stop_Codon: stopCodon.stopCodon || "N/A", Stop_bp: stopCodon.stopCodonBP || "N/A", GeneMarkS: `https://phagesdb.org/genemarks/${cleanedPhagename}#page=${page}`, GeneMarkHost: `https://phagesdb.org/genemarkhost/${cleanedPhagename}/5/#page=${page}`, Frame: Frame, Page: page, DNA: startCodon.gapDNASequence || "", Protein: startCodon.gapProteinSequence || "" }); } } } } } return result; }3d:T4cb,// Reactive filtered data cell filteredData = { const data = await findGenesInGapSequences; return data.filter((item) => { // Check if the item is "GenomeEnd" const isGenomeEnd = item.name === "GenomeEnd"; // Apply phage filtering for all items const phageFilter = filterGeneGapsByPhage === "All phages" || item.phagename === filterGeneGapsByPhage; // Handle ORF filtering for items that are not "GenomeEnd" const orfFilterTopStrand = !isGenomeEnd && item.stopCodonsTopStrand?.some((stopCodon) => stopCodon.startCodons?.some( (startCodon) => selectORFLength === "All" || startCodon.ORF >= selectORFLength ) ); const orfFilterBottomStrand = !isGenomeEnd && item.stopCodonsBottomStrand?.some((stopCodon) => stopCodon.startCodons?.some( (startCodon) => selectORFLength === "All" || startCodon.ORF >= selectORFLength ) ); // If "GenomeEnd," only apply the phage filter if (isGenomeEnd) { return phageFilter; } // For all other items, apply both phage and ORF filters return phageFilter && (orfFilterTopStrand || orfFilterBottomStrand); }); }3e:T76b,function dnaToProtein(dnaSequence) { // Define codon table const codonTable = { TTT: "F", TTC: "F", TTA: "L", TTG: "L", CTT: "L", CTC: "L", CTA: "L", CTG: "L", ATT: "I", ATC: "I", ATA: "I", ATG: "M", GTT: "V", GTC: "V", GTA: "V", GTG: "V", TCT: "S", TCC: "S", TCA: "S", TCG: "S", CCT: "P", CCC: "P", CCA: "P", CCG: "P", ACT: "T", ACC: "T", ACA: "T", ACG: "T", GCT: "A", GCC: "A", GCA: "A", GCG: "A", TAT: "Y", TAC: "Y", TAA: "*", TAG: "*", CAT: "H", CAC: "H", CAA: "Q", CAG: "Q", AAT: "N", AAC: "N", AAA: "K", AAG: "K", GAT: "D", GAC: "D", GAA: "E", GAG: "E", TGT: "C", TGC: "C", TGA: "*", TGG: "W", CGT: "R", CGC: "R", CGA: "R", CGG: "R", AGT: "S", AGC: "S", AGA: "R", AGG: "R", GGT: "G", GGC: "G", GGA: "G", GGG: "G" }; let proteinSequence = ""; let isFirstCodon = true; // Flag to track the first codon // Iterate through the dnaSequence in steps of 3 characters (codons) for (let i = 0; i < dnaSequence.length; i += 3) { const codon = dnaSequence.substr(i, 3); // Get the current codon const aminoAcid = codonTable[codon] || "?"; // Use "?" for unknown codons // Ensure the first codon translates to Methionine (M) if not already if (isFirstCodon) { if (aminoAcid === "M") { proteinSequence += "M"; // Add Methionine if the first codon correctly encodes for it } else { proteinSequence += "M"; // Force Methionine at the start if the first codon does not encode for it } isFirstCodon = false; // Update flag after processing the first codon } else { proteinSequence += aminoAcid; // Add the amino acid to the sequence } } return proteinSequence; }3f:T637,proteinLengthData = proteinLengths.reduce( (acc, { phamName, proteinLength, genefunction }) => { // Cache the current pham data for quick access let phamData = acc[phamName]; if (!phamData) { acc[phamName] = { maxProteinLength: proteinLength, maxCount: 1, minProteinLength: proteinLength, minCount: 1, lengthDifference: 0, genefunction: genefunction || "Unknown", // Assuming a default function if empty phageCount: 1, uniqueProteinLengths: new Set([proteinLength]) }; } else { // Update max if (proteinLength > phamData.maxProteinLength) { phamData.maxProteinLength = proteinLength; phamData.maxCount = 1; } else if (proteinLength === phamData.maxProteinLength) { phamData.maxCount++; } // Update min if (proteinLength < phamData.minProteinLength) { phamData.minProteinLength = proteinLength; phamData.minCount = 1; } else if (proteinLength === phamData.minProteinLength) { phamData.minCount++; } // Increment phage count phamData.phageCount++; // Update gene function if necessary if (genefunction !== "" && genefunction !== phamData.genefunction) { phamData.genefunction = genefunction; } // Update the max-min difference phamData.lengthDifference = phamData.maxProteinLength - phamData.minProteinLength; // Update unique protein lengths phamData.uniqueProteinLengths.add(proteinLength); } return acc; }, {} )40:T91c,analyzeGaps = { // Filter out any pham entries with only one item before processing const filteredPhamEntries = phage_geneByPham.filter((phamEntry) => { if (filterGapAnalysisPhages === "All phages") { return phamEntry.phage_gene.length > 1; } else { return ( phamEntry.phage_gene.length > 1 && phamEntry.phage_gene.some( (gene) => gene.phageName === filterGapAnalysisPhages ) ); } }); // Function to analyze each pham entry const analyzedPhamEntries = filteredPhamEntries.map((phamEntry) => { const gaps = phamEntry.phage_gene.map((gene) => gene.gap); // Extract all gap values // Compute frequency of each gap const gapCount = gaps.reduce((acc, gap) => { acc[gap] = (acc[gap] || 0) + 1; return acc; }, {}); // Determine the most common gap and its frequency let maxCount = 0; let mostCommonGap = null; Object.entries(gapCount).forEach(([gap, count]) => { if (count > maxCount) { maxCount = count; mostCommonGap = parseInt(gap); } }); const modePercentage = (maxCount / gaps.length) * 100; // Percentage of the most common gap const totalItems = phamEntry.phage_gene.length; // Total number of items in each phage_gene array // Prepare non-common gap entries to be set as individual fields const nonCommonGaps = phamEntry.phage_gene.filter( (gene) => gene.gap !== mostCommonGap ); // Returning the result for this pham with dynamic fields for non-common genes and gaps const result = { Pham: parseInt(phamEntry.pham, 10), //This converts the string to an integer for sorting numerically in the table TotalPhages: totalItems, MostCommonGap: mostCommonGap, TimesMostCommonGapCalled: maxCount, PercentCalled: `${modePercentage.toFixed(2)}%` }; nonCommonGaps.forEach((gene, index) => { result[ `NonCommonGapGene${index + 1}` ] = `${gene.phageName}_CDS_${gene.gene}`; result[`Gap${index + 1}`] = gene.gap; }); return result; }); // Order the analyzed pham entries by PercentFound or modePercent const orderedPhamEntries = analyzedPhamEntries.sort((a, b) => { return parseFloat(b.PercentCalled) - parseFloat(a.PercentCalled); }); return orderedPhamEntries; }41:T9d6,analyzeFunctions = { // Filter out any pham entries with only one item before processing const filteredPhamEntries = phage_geneByPham.filter((phamEntry) => { if (filterFunctionAnalysisPhages === "All phages") { return phamEntry.phage_gene.length > 1; } else { return ( phamEntry.phage_gene.length > 1 && phamEntry.phage_gene.some( (gene) => gene.phageName === filterFunctionAnalysisPhages ) ); } }); // Function to analyze each pham entry const analyzedPhamEntries = filteredPhamEntries.map((phamEntry) => { const geneFunction = phamEntry.phage_gene.map((gene) => gene.geneFunction); // Extract all function values // Compute frequency of each gap const geneFunctionCount = geneFunction.reduce((acc, geneFunction) => { acc[geneFunction] = (acc[geneFunction] || 0) + 1; return acc; }, {}); // Determine the most common GeneFunction and its frequency let maxCount = 0; let mostCommonGeneFunction = null; Object.entries(geneFunctionCount).forEach(([geneFunction, count]) => { if (count > maxCount) { maxCount = count; mostCommonGeneFunction = geneFunction.toString(); // Convert to string } }); const modePercentage = (maxCount / geneFunction.length) * 100; // Percentage of the most common function const totalItems = phamEntry.phage_gene.length; // Total number of items in each phage_gene array // Prepare non-common gap entries to be set as individual fields const nonCommongGeneFunction = phamEntry.phage_gene.filter( (gene) => gene.geneFunction !== mostCommonGeneFunction ); // Returning the result for this pham with dynamic fields for non-common genes and function const result = { Pham: parseInt(phamEntry.pham, 10), TotalPhages: totalItems, MostCommonGeneFunction: mostCommonGeneFunction, TimesMostCommonGeneFunctionCalled: maxCount, PercentCalled: `${modePercentage.toFixed(2)}%` }; nonCommongGeneFunction.forEach((gene, index) => { result[ `NonCommonGeneFunctionGene${index + 1}` ] = `${gene.phageName}_CDS_${gene.gene}`; result[`geneFunction${index + 1}`] = gene.geneFunction; }); return result; }); // Order the analyzed pham entries by PercentFound or modePercent const orderedPhamEntries = analyzedPhamEntries.sort((a, b) => { return parseFloat(b.PercentCalled) - parseFloat(a.PercentCalled); }); return orderedPhamEntries; }42:Ta27,analyzeLengths = { // Filter out any pham entries with only one item before processing const filteredPhamEntries = phage_geneByPham.filter((phamEntry) => { if (filterGeneLengthAnalysisPhages === "All phages") { return phamEntry.phage_gene.length > 1; } else { return ( phamEntry.phage_gene.length > 1 && phamEntry.phage_gene.some( (gene) => gene.phageName === filterGeneLengthAnalysisPhages ) ); } }); // If no items are returned, return an empty array if (filteredPhamEntries.length === 0) { console.log("No results found."); return []; } // Analyze each pham entry const analyzedPhamEntries = filteredPhamEntries.map((phamEntry) => { const geneLength = phamEntry.phage_gene.map((gene) => gene.length); // Extract all length values // Compute frequency of each length const geneLengthCount = geneLength.reduce((acc, length) => { acc[length] = (acc[length] || 0) + 1; return acc; }, {}); // Determine the most common GeneLength and its frequency let maxCount = 0; let mostCommonGeneLength = null; Object.entries(geneLengthCount).forEach(([length, count]) => { if (count > maxCount) { maxCount = count; mostCommonGeneLength = parseInt(length, 10); } }); const modePercentage = (maxCount / geneLength.length) * 100; // Percentage of the most common gap const totalItems = phamEntry.phage_gene.length; // Total number of items in each phage_gene array // Prepare non-common gap entries to be set as individual fields const nonCommonGeneLengthGenes = phamEntry.phage_gene.filter( (gene) => gene.length !== mostCommonGeneLength ); // Returning the result for this pham with dynamic fields for non-common genes and gaps const result = { Pham: parseInt(phamEntry.pham, 10), // Convert to an integer for sorting numerically TotalPhages: totalItems, MostCommonGeneLength: mostCommonGeneLength, TimesMostCommonGeneLengthCalled: maxCount, PercentCalled: `${modePercentage.toFixed(2)}%` }; nonCommonGeneLengthGenes.forEach((gene, index) => { result[ `NonCommonGeneLengthGene${index + 1}` ] = `${gene.phageName}_CDS_${gene.gene}`; result[`geneLength${index + 1}`] = gene.length; }); return result; }); // Order the analyzed pham entries by PercentCalled const orderedPhamEntries = analyzedPhamEntries.sort((a, b) => { return parseFloat(b.PercentCalled) - parseFloat(a.PercentCalled); }); return orderedPhamEntries; } 43:T806,phage_geneByPham = { // Create a map to store the combined data by pham const phamMap = new Map(); // Pre-process genesbycluster to organize data for quick access const geneLookup = new Map(); phageGenesToHarmonize.forEach((gene) => { const key = `${gene.phamName}_${gene.phageID}`; // Create a unique key for each gene if (!geneLookup.has(key)) { geneLookup.set(key, []); } geneLookup.get(key).push(gene); }); // Loop through each pham phamWithPhages.forEach((phamItem) => { // Initialize the array for this pham if it doesn't exist in the map if (!phamMap.has(phamItem.pham)) { phamMap.set(phamItem.pham, []); } // Loop through each phageName within the current pham phamItem.phageName.forEach((phageName) => { // Efficiently find the corresponding genes by constructing the key const key = `${phamItem.pham}_${phageName}`; const genes = geneLookup.get(key) || []; genes.forEach((gene) => { let name = gene.name; let geneFunction = gene.genefunction || "NKF"; // NKF = No Known Function let gap = gene.gap || 0; let length; if (gene.direction === "forward") { length = gene.stop - gene.start + 1; } else { length = gene.start - gene.stop + 1; } // Get the current array for this pham from the map and add the new object phamMap.get(phamItem.pham).push({ phageName: phageName, gene: name, geneFunction: geneFunction, gap: gap, length: length }); }); // Handle case where no genes are found if (genes.length === 0) { phamMap.get(phamItem.pham).push({ phageName: phageName, gene: "-", geneFunction: "-", gap: "-", length: "-" }); } }); }); // Convert the map into an array of objects const combinedData = Array.from(phamMap, ([pham, phage_gene]) => ({ pham, phage_gene })); return combinedData; }44:T6c2,// Format Data for the Start Sites Organization Inputs table function prepareRow(item, showGeneNumber, displayOption) { const newRow = { Pham: Number(item.pham) }; const shouldAppendGeneNumber = showGeneNumber !== "No"; const phageGeneMap = {}; // To track phams which have multiple entries for the same phageName for (let i = 0; i < item.phage_gene.length; i++) { const pg = item.phage_gene[i]; let displayValue = null; //Set the display options if (displayOption === "Gene") { displayValue = Number(pg.gene); } else if (displayOption === "Gap") { displayValue = Number(pg.gap); } else if (displayOption === "Function") { displayValue = pg.geneFunction; } else if (displayOption === "Length") { displayValue = Number(pg.length); } else { displayValue = Number(pg.gene); // Default to displaying gene as a number } // Ensure gene is three digits with leading zeros for numerical sorting const formattedGene = pg.gene.toString().padStart(3, "0"); //Append Gene Number in braces infront of the display value to show which gene the item is associated with //If shouldAppendGeneNumber = Yes if (shouldAppendGeneNumber) { displayValue = `(${formattedGene}) ${displayValue}`; } if (phageGeneMap[pg.phageName]) { // If the phageName already exists, append the new gene with a comma phageGeneMap[pg.phageName] += `, ${displayValue}`; } else { // Otherwise, create a new entry phageGeneMap[pg.phageName] = displayValue; } } // Add the phageName data to newRow for (const [phageName, geneList] of Object.entries(phageGeneMap)) { newRow[phageName] = geneList; } return newRow; }45:T410,clusterSpecificPhamilies = { let clusterSpecificPhamilies = []; let phamiliesObj = {}; phamilies.forEach((phamily) => { let phamName = phamily.PhamID; let size = phamily.size; phamiliesObj[phamName] = size; }); let genesByCluster = await getPhameratorData( dataset, `/genesbycluster/${selectedCluster}`, apiKey ); let uniqueNames = new Set(genesByCluster.map((gene) => gene.phamName)); for (let phamName of uniqueNames) { let countPhamMembersThisCluster = genesByCluster.filter( (gene) => gene.phamName === phamName ).length; let phamSize = phamiliesObj[phamName]; if (countPhamMembersThisCluster === phamSize) { let phamColor = genesByCluster.filter( (gene) => gene.phamName === phamName )[0].phamColor; clusterSpecificPhamilies.push({ phamName: +phamName, size: phamSize, phamColor: phamColor }); } } clusterSpecificPhamilies.sort((a, b) => a.phamName - b.phamName); return clusterSpecificPhamilies; }46:T52c,GetPhageGapSequences = { let GenesGroupedByPham = {}; // Loop through each phage in the selected cluster and get the phage's DNA sequence for (const phage of dataPhages) { let genomeData = await getPhameratorData( dataset, `/genome/${phage.phagename}/`, apiKey ); let previousStart = 0; if (genomeData && genomeData.sequence) { for (const gene of genomeData.genes) { let stop = gene.start - 1; let start = previousStart; let geneSequence = stop <= start ? `Negative Gap: ${gene.gap}` : genomeData.sequence.substring(start, stop); let geneInfo = { phagename: phage.phagename, gapSequence: geneSequence, name: gene.name, geneStart: gene.start, geneStop: gene.stop, gapStart: start, gapStop: stop, direction: gene.direction, pham: gene.phamName, gap: gene.gap }; previousStart = gene.stop; if (!GenesGroupedByPham[gene.phamName]) { GenesGroupedByPham[gene.phamName] = { genes: [], geneFunction: gene.genefunction }; } GenesGroupedByPham[gene.phamName].genes.push(geneInfo); } } } return GenesGroupedByPham; }47:T452,GetAllPhageDNASequences = { let GenesGroupedByPham = {}; for (const phage of dataPhages) { let genomeData = await getPhameratorData( dataset, `/genome/${phage.phagename}/`, apiKey ); let previousStart = 0; if (genomeData && genomeData.sequence) { for (const gene of genomeData.genes) { let stop = gene.start - 1; let start = previousStart; let geneSequence = stop <= start ? `Gap: ${gene.gap}` : genomeData.sequence.substring(stop, start); let geneInfo = { phagename: phage.phagename, gapSequence: geneSequence, name: gene.name, start: start, stop: stop, direction: gene.direction }; previousStart = gene.stop; if (!GenesGroupedByPham[gene.phamName]) { GenesGroupedByPham[gene.phamName] = { genes: [], geneFunction: gene.genefunction }; } GenesGroupedByPham[gene.phamName].genes.push(geneInfo); } } } return GenesGroupedByPham; 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2c:{"id":"0fd237126fd99985","slug":"pharmonizer","title":"Pharmonizer (Phage 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(Phage Harmonization)","cells":[{"id":0,"value":"# Pharmonizer (Phage Harmonization)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":5529,"value":"$2e","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3661,"value":"Terms of use: To use this notebook, log in below with your phamerator.org email address and password. (If needed, you can register at https://classic.phamerator.org/sign-up. Use of phamerator.org, the phamerator.org API, or data stored in the phamerator.org database, whether the use occurs here on https://observablehq.com or elsewhere, constitutes your agreement to the terms and policies of both phamerator.org and the SEA-PHAGES program's phagesdb.org. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1595,"value":"---\n## Select Database and Cluster to Pharmonize\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":11327,"value":"viewof dataset = Inputs.select(user ? user.datasets.sort() : [], {\n label: \"Phamerator data set\",\n value: user?.datasets?.includes(\"Actino_Draft\")\n ? \"Actino_Draft\"\n : user?.datasets?.[0]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":38,"value":"// Select what cluster of phage data you want\nviewof selectedCluster = Inputs.select(\n clusters.map((cluster) => cluster.name),\n { label: \"Cluster\", value: \"AZ\" }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9995,"value":"Clusters 'A' and 'B' are large and may take a minute to load - please be patient.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":9851,"value":"PhagesDB Cluster ${selectedCluster}","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10578,"value":"---\n## Select & Load Phage Data for Cluster Harmonization\n- Select a curated list of verified phages and the phage(s) you want to evaluate.\n- If there is no curated list, then consider adding all the annotated phages.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10584,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10587,"value":"viewof refreshButton = html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9928,"value":"\n\n\n\nPhage Gene Analysis\n\n\n\n\n\n\n\n\n","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3533,"value":"---\n## Track or View Cluster Harmonization Data\n- Download the grid for Google Sheets or Excel:\n 1. Mouse over the table below\n 2. Click the 3 vertical dots (located on the left)\n 3. Select \"download CSV\" and open in Excel or Sheets","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":8611,"value":"viewof selectSpreadSheetDisplayOption = Inputs.radio(\n [\"Gene\", \"Function\", \"Gap\", \"Length\"],\n {\n label: \"Display options:\",\n value: \"Gene\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8641,"value":"viewof selectSpreadSheetDisplayOptionShowGeneNumber = Inputs.radio(\n [\"No\", \"Yes\"],\n {\n label: \"Show Gene Number\",\n value: \"No\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3705,"value":"\"Phams:\" +\n phamWithPhages.length +\n \" Phages:\" +\n (phageGenesToHarmonize_UniquePhages.length - 1) +\n \" Genes:\" +\n phageGenesToHarmonize.length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8119,"value":"cluster_grid = Inputs.table(\n phage_geneByPham.map((item) =>\n prepareRow(\n item,\n selectSpreadSheetDisplayOptionShowGeneNumber,\n selectSpreadSheetDisplayOption\n )\n ),\n {\n sort: (a, b) => a.phageName - b.phageName,\n format: {\n Pham: (pham) =>\n htl.html`${pham}`\n },\n layout: \"auto\",\n rows: 20\n }\n)\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2267,"value":"---\n## Phams with more than one function\nGenes in a pham should have the same function. Listed below are phams with multiple functions.\n
For more information on phams.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":6428,"value":"viewof filterPhamsWithDifferentFunctions = Inputs.select(\n phageGenesToHarmonize_UniquePhages,\n {\n label: `Select Phage:`\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2378,"value":"viewof showPhages = Inputs.radio([\"Functions Only\", \"Functions and Phages\"], {\n label: \"Display Options\",\n value: \"Functions Only\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3693,"value":"phamFunctionsTable.length + \" phams have more than one function called.\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6600,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8583,"value":"*Pham numbers are subject to change when the Phamerator database updates. Occasionally a pham hyperlink may be broken.\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2911,"value":"---\n## Review a Gap for a Gene\nThis script shows open reading frames (ORFs) in gaps. \n\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":11189,"value":"- SEA-PHAGES steps to evaluate a gap or a protein \n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":7931,"value":"- Set the DNA sequence you want to examine for ORFs","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":11228,"value":"![image@24.png](${await FileAttachment(\"image@24.png\").url()})","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":8034,"value":"viewof previousGeneOverlap = Inputs.range([0, 40], {\n value: 15,\n step: 1,\n label: \"Previous overlap:\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10340,"value":"viewof nextGeneOverlap = Inputs.range([0, 40], {\n value: 15,\n step: 1,\n label: \"Next overlap:\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7135,"value":"viewof selectORFLength = Inputs.range([0, 250], {\n value: 120,\n step: 1,\n label: \"Evaluate gaps greater than:\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11186,"value":"* How to review the returned ORF data\n 1. Click a link in the GeneMarkS or GeneMarkHost column to view coding potential.\n 2. Click a link in the DNA column to run a BlastN search.\n 6. Click a link in the Protein column to run a BlastP search or copy the sequence in HHPred\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":7199,"value":"viewof filterGeneGapsByPhage = Inputs.select(\n [\"All phages\"].concat(\n phageGenesToHarmonize_UniquePhages_DraftNaming\n .map((phage) => phage.phagename)\n .sort()\n ),\n {\n label: `Filter by Phage`\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7429,"value":"viewof showFullSequences = Inputs.radio([\"Yes\", \"No\"], {\n label: \"Display full DNA/Protein sequence\",\n value: \"No\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3702,"value":"parseGapSequences.length +\n \" ORFs detected in the gaps of phage \" +\n filterGeneGapsByPhage","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7322,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7472,"value":"\n","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2164,"value":"---\n## Tandem Start Site Check\nDisplays genes where the 2nd of two tandem start codons is NOT chosen.\n
(i.e. ATG, GTG, or TTG is followed by another ATG, GTG, or TTG).\n- Mass spec data supports the selection of second tandem starts.
- See the SEA-PHAGES Bioinformatics Guide.\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":4167,"value":"viewof filterTandemStarts = Inputs.select(phageGenesToHarmonize_UniquePhages, {\n label: `Filter Results by Phage:`\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3689,"value":"{\n if (filterTandemStarts == \"All phages\") {\n return (\n getTandemStartSites.length +\n \" gene(s) with the first tandem start selected\"\n );\n } else {\n return (\n filterTandemStartSites.length +\n \" gene(s) with the first tandem start selected\"\n );\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2178,"value":"tandemStarSiteResults = Inputs.table(\n filterTandemStarts === \"All phages\"\n ? getTandemStartSites\n : filterTandemStartSites,\n {\n sort: \"PhageName\",\n format: {\n PhageName: (PhageName, Name) =>\n htl.html`${PhageName}`,\n\n Starterator: (Pham) =>\n htl.html`${Pham}`\n },\n layout: \"auto\",\n rows: 15\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5190,"value":"---\n## Gene Length Anomalies\nShows the difference between the longest and shortest protein length in a Pham.
Genes in a Pham should have similar protein lengths. \n

Legend explaining the columns\n- MaxProteinLength: Longest protein sequence (# of phages with max length).\n- MinProteinLength: Shortest protein sequence (# of phages with min length).\n- Difference = Longest protein length - shortest protein length.\n- PhageCount: The number of cluster specific phages in the Pham.\n- UniqueProteinLengths: The number of different protein lengths (aa) in the pham.\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":5192,"value":"Inputs.table(\n formattedProteinLengthData.sort((a, b) => b.Difference - a.Difference),\n {\n format: {\n phamName: (phamName) =>\n htl.html`${phamName}`\n },\n layout: \"auto\",\n rows: 15\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10031,"value":"---\n## Overlap/Gap Analysis\n1. Identifies the most common gene Gap/Overlap in a pham and\n2. Details phage genes lacking these common gaps.\n
*Phams where only one of the selected phages is present will not be shown","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10231,"value":"viewof filterGapAnalysisPhages = Inputs.select(\n phageGenesToHarmonize_UniquePhages,\n {\n label: `Select Phage:`\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10057,"value":"viewof showPhamGaps = Inputs.radio(\n [\"Different lengths\", \"All the same length\"],\n {\n label: \"Display phams where gene gap sizes are:\",\n value: \"Different lengths\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10222,"value":"$${rowCountGeneGapAnalysis} phams","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10029,"value":"geneGapAnalysisResults = {\n const filteredData =\n showPhamGaps === \"Different lengths\"\n ? analyzeGaps.filter((d) => d.PercentCalled !== \"100.00%\")\n : analyzeGaps.filter((d) => d.PercentCalled == \"100.00%\");\n // Check if filteredData is empty\n if (filteredData.length === 0) {\n return [0];\n }\n\n // Get the length dynamically\n const length = Object.keys(filteredData[0]).length;\n\n return Inputs.table(filteredData, {\n format: {\n Pham: (pham) =>\n htl.html`${pham}`,\n ...Array.from({ length }, (_, i) => i).reduce((acc, idx) => {\n const geneKey = `NonCommonGapGene${idx + 1}`;\n const gapKey = `Gap${idx + 1}`;\n acc[geneKey] = (gene) =>\n gene\n ? htl.html`${gene}`\n : \"\";\n\n return acc;\n }, {})\n },\n layout: \"auto\",\n rows: 15\n });\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10077,"value":"---\n## Gene Function Analysis\n1. Identifies the most common gene Function in a pham and\n2. Details phage genes lacking the most common function\n
*Phams where only one of the selected phages is present will not be shown","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10236,"value":"viewof filterFunctionAnalysisPhages = Inputs.select(\n phageGenesToHarmonize_UniquePhages,\n {\n label: `Select Phage:`\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10085,"value":"viewof showPhamFunctions = Inputs.radio(\n [\"Different functions\", \"All the same function\"],\n {\n label: \"Display phams where gene functions are:\",\n value: \"Different functions\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10224,"value":"$${rowCounrGeneFunctionAnalysis} phams","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10087,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10120,"value":"---\n## Gene Length Analysis\n1. Identifies the most common gene Length in a pham and\n2. Details phage genes lacking the most common gene Length\n
*Phams where only one of the selected phages is present will not be shown","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10238,"value":"viewof filterGeneLengthAnalysisPhages = Inputs.select(\n phageGenesToHarmonize_UniquePhages,\n {\n label: `Select Phage:`\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10122,"value":"viewof showPhamLengths = Inputs.radio(\n [\"Different lengths\", \"All the same length\"],\n {\n label: \"Display phams where gene lengths are:\",\n value: \"Different lengths\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10228,"value":"$${rowCountGeneLengthAnalysis} phams","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10125,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5683,"value":"---\n# Download Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":6200,"value":"### Download DNA Sequences of Phages in a Cluster/Subcluster (.fasta) \n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":9937,"value":"*Note:* Some clusters, like AZ, have subclusters (AZ1, AZ2, AZ3...). Draft phages may be assigned to the parent cluster (AZ) and have a subcluster = none.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":5697,"value":"viewof selectedDataset = Inputs.select(user.datasets.sort(), {\n label: \"Select Phamerator Database:\",\n value: \"Actino_Draft\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5687,"value":"viewof selectedDataCluster = Inputs.select(\n clusters.map((cluster) => cluster.name),\n { label: \"Select a Cluster:\", value: \"AZ\" }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9920,"value":"viewof selectedSubcluster_ForPhageDNASequenceDownload = Inputs.select(\n subclusters_ForPhageDNADownload,\n {\n label: \"Select a Subcluster:\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9394,"value":"viewof showClusterDownload_DraftPhages = Inputs.radio([\"Yes\", \"No\"], {\n label: \"Include Draft Phages:\",\n value: \"Yes\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9471,"value":"$${phagesByCluster_ClusterDNASequenceDownloads_Filtered.length} Cluster '${selectedDataCluster}' phages selected ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":5945,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5817,"value":"---\n### Download DNA or Protein Sequences of Phages in a Pham (.fasta)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":6423,"value":"viewof selectedDataClusterForPhamDownloads = Inputs.select(\n clusters.map((cluster) => cluster.name),\n { label: \"Select a Cluster:\", value: \"AZ\" }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5606,"value":"viewof selectedDataPham = Inputs.select(phamsbyDataCluster, {\n label: \"Select a Pham:\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6066,"value":"viewof filterPhamDownloadData = Inputs.radio(\n [\"All pham genes\", \"Cluster genes only\"],\n {\n label: \"Filter pham genes\",\n value: \"All pham genes\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9558,"value":"{\n let genesCount;\n\n if (filterPhamDownloadData === \"Cluster genes only\") {\n genesCount = phamData_IncludingOnlyPhagesFromSelectedCluster.length;\n return html`

\n ${genesCount} cluster \"${selectedDataClusterForPhamDownloads}\" genes in pham ${selectedDataPham}\n

`;\n } else {\n genesCount = phamily.length;\n return html`

\n ${genesCount} genes in pham ${selectedDataPham}\n

`;\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9544,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6077,"value":"$36","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6190,"value":"Download cluster \"${selectedDataClusterForPhamDownloads}\" gap DNA sequences upstream of genes in pham ${selectedDataPham}","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":6166,"value":"Inputs.button(\"Download Gaps Upstream of Pham \" + selectedDataPham, {\n reduce: (d) => downloadAllPhamGaps(selectedDataPham)\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10141,"value":"---\n# Data Tools","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10139,"value":"Multiple Sequence Alignment (MSA) Tools\n- MUSCLE
\n\nAlphaFold\n- AlphaFold Server","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":399,"value":"---\n# Data Sources","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":6613,"value":"### Data for Dropdown boxes (UI) and Functions\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":43,"value":"clusters = dataset && apiKey\n ? await getPhameratorData(dataset, \"/clusters\", apiKey)\n : []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9706,"value":"subclusters = phagesByCluster.reduce((subClusters, phage) => {\n if (!subClusters.includes(phage.clusterSubcluster)) {\n subClusters.push(phage.clusterSubcluster);\n }\n return subClusters;\n}, [])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":292,"value":"phagesByCluster = getPhameratorData(\n dataset,\n `/phagesbycluster/${selectedCluster}`,\n apiKey\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":534,"value":"phageGenesByCluster = await getPhameratorData(\n dataset,\n `/genesbycluster/${selectedCluster}`,\n apiKey\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10596,"value":"mutable phageGenesToHarmonize = {\n const selectedPhages1Listbox = document.querySelector(\"#selectedPhages1\");\n if (!selectedPhages1Listbox) {\n console.error(\"Listbox with id 'selectedPhages1' not found.\");\n return [];\n }\n\n const selectedPhages = Array.from(selectedPhages1Listbox.options).map(\n (option) =>\n option.value.endsWith(\"_Draft\")\n ? option.value.replace(\"_Draft\", \"\")\n : option.value\n );\n\n const matchingPhams = phageGenesByCluster.filter((gene) =>\n selectedPhages.includes(gene.phageID)\n );\n\n return matchingPhams;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10628,"value":"//Create a list of phages (unique) from the phageGenesToHarmonize Dataset. This phage list will be used in the comboboxes to filter the data\nphageGenesToHarmonize_UniquePhages = [\n \"All phages\",\n ...new Set(phageGenesToHarmonize.map((item) => item.phageID))\n]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10652,"value":"//This code adds \"_Draft\" back to the phage names of phages that are Draft phages. This is needed to find phages in the data for finding Gap information\nphageGenesToHarmonize_UniquePhages_DraftNaming = phagesByCluster.filter(\n (item) => {\n const phagename = item?.phagename; // Ensure item and phagename exist\n if (typeof phagename !== \"string\") return false; // Skip if phagename is not a string\n\n const normalizedPhagename = phagename.endsWith(\"_Draft\")\n ? phagename.replace(\"_Draft\", \"\")\n : phagename;\n\n return phageGenesToHarmonize_UniquePhages.includes(normalizedPhagename);\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6435,"value":"//IS THIS CODE STILL NEEDED?\n//Create a list of phages for the dropdown comboboxes.\n//Remove \"_Draft\" from the phage name\n//Add \"All Phages\" to the top of the list\nphagesByClusterFormatted = [\"All phages\"].concat(\n phagesByCluster\n //Some phages have _Draft in the name. Remnove this so the filter can work using just the phage name\n .map((phage) => phage.phagename.replace(\"_Draft\", \"\"))\n .sort()\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8997,"value":"//IS THIS CODE STILL NEEDED?\n//Create a list of phages for the dropdown comboboxes.\n//Remove \"_Draft\" from the phage name\nphagesByCluster_RemoveDraftFromName = phagesByCluster\n //Some phages have _Draft in the name. Remnove this so the filter can work using just the phage name\n .map((phage) => phage.phagename)\n .sort()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10590,"value":"### Code for the button \"Update Harmonization Data\"","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10592,"value":"// Add an event listener to the button 'Update Harmonization Data'\n(viewof refreshButton.onclick = () => {\n mutable phageGenesToHarmonize = updatePhageGenesToHarmonize();\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10594,"value":"// Function to fetch and update the array\nfunction updatePhageGenesToHarmonize() {\n const selectedPhages1Listbox = document.querySelector(\"#selectedPhages1\");\n if (!selectedPhages1Listbox) {\n console.error(\"Listbox with id 'selectedPhages1' not found.\");\n return [];\n }\n\n const selectedPhages = Array.from(selectedPhages1Listbox.options).map(\n (option) =>\n option.value.endsWith(\"_Draft\")\n ? option.value.replace(\"_Draft\", \"\")\n : option.value\n );\n\n const matchingPhams = phageGenesByCluster.filter((gene) =>\n selectedPhages.includes(gene.phageID)\n );\n\n return matchingPhams;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1986,"value":"### Data for Tandem Start Sites","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":9725,"value":"getTandemStartSites = {\n const validCodons = new Set([\"ATG\", \"GTG\", \"TTG\"]); // Using a Set for faster lookups\n\n return phageGenesToHarmonize.reduce((results, gene) => {\n const secondCodon = gene.sequence.substring(3, 6); // Only extract once and use it multiple times\n if (validCodons.has(secondCodon)) {\n // Using `.has` method of Set for O(1) complexity\n results.push({\n PhageName: gene.phageID + \"_CDS_\" + gene.name,\n Starterator: parseInt(gene.phamName, 10),\n Start: gene.start,\n First_Start: gene.sequence.substring(0, 3), // Moved inside the condition\n Second_Start: secondCodon,\n DNA_Sequence: gene.sequence\n });\n }\n return results;\n }, []);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8863,"value":"// Filter the phage data according to the selected phage in the filterTandemStarts combobox\nfilterTandemStartSites = getTandemStartSites\n .map((d) => ({\n PhageName: d.PhageName, // Format the PhageName value for the PhagesDB.org URL to the phage gene's webpage\n Starterator_Report: d.Pham,\n Start: d.Start,\n First_Start: d.First_Start,\n Second_Start: d.Second_Start,\n DNA_Sequence: d.DNA_Sequence\n }))\n .filter(\n (d) =>\n filterTandemStarts === \"All phages\" ||\n d.PhageName.includes(filterTandemStarts)\n )","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1935,"value":"### Data for Pham Functions\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2327,"value":"$37","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6578,"value":"//Filter the phamsWithDifferentFunctionsByCluster array ...\n//to only include phams which contain the phage in the filterPhamsWithDifferentFunctions\nphamsWithDifferentFunctionsByPhage = {\n //Do not run the code it \"All phages\" is selected - return an empty array\n if (filterPhamsWithDifferentFunctions !== \"All phages\") {\n const result = phamsWithDifferentFunctionsByCluster.filter((pham) =>\n pham.details.some((detail) =>\n detail.genes.some(\n (gene) => gene.phageID.trim() === filterPhamsWithDifferentFunctions\n )\n )\n );\n\n // Return the full data for each pham that meets the condition\n return result;\n } else {\n return []; // Return an empty array when \"All phages\" is selected.\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8555,"value":"//List of Draft Phages\n//If searching by a phage which is a Draft phage then remove that name from this list so it is included in the search\ndraftPhagesByCluster = new Set(\n phagesByCluster\n .filter((phage) => {\n if (phagesByClusterFormatted === \"All phages\") {\n // Include all phages where the phagename ends with \"_Draft\"\n return phage.phagename.endsWith(\"_Draft\");\n } else {\n // Include all phages ending in \"_Draft\" except the specific phage that matches the formatted string\n return (\n phage.phagename.endsWith(\"_Draft\") &&\n phage.phagename !== filterPhamsWithDifferentFunctions + \"_Draft\"\n );\n }\n })\n .map((phage) => phage.phagename.replace(\"_Draft\", \"\"))\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8559,"value":"annotatedPhageGenesByCluster = (\n await getPhameratorData(dataset, `/genesbycluster/${selectedCluster}`, apiKey)\n).filter((gene) => !draftPhagesByCluster.has(gene.phageID))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8455,"value":"$38","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8571,"value":"//Filter the phamsWithDifferentFunctionsByCluster array ...\n//to only include phams which contain the phage in the filterPhamsWithDifferentFunctions\nphamsWithDifferentFunctionsByAnnotatedPhages_FilterByPhage = {\n //Do not run the code it \"All phages\" is selected - return an empty array\n if (filterPhamsWithDifferentFunctions !== \"All phages\") {\n const result = phamsWithDifferentFunctionsByAnnotatedPhages.filter((pham) =>\n pham.details.some((detail) =>\n detail.genes.some(\n (gene) => gene.phageID.trim() === filterPhamsWithDifferentFunctions\n )\n )\n );\n\n // Return the full data for each pham that meets the condition\n return result;\n } else {\n return []; // Return an empty array when \"All phages\" is selected.\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9832,"value":"#### Code for displaying the Pham Function data in the Inputs.Table","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":9836,"value":"function determineDataSource() {\n return filterPhamsWithDifferentFunctions === \"All phages\"\n ? phamsWithDifferentFunctionsByCluster\n : phamsWithDifferentFunctionsByPhage;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9839,"value":"$39","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9842,"value":"function formatFunctionWithFilteredPhages(detail) {\n const filteredGenes = detail.genes.filter(gene => gene.phageID.trim() === filterPhamsWithDifferentFunctions);\n const phageIDsWithNames = filteredGenes.map(gene => `${gene.phageID.trim()}_${gene.name}`).join(\", \");\n return `${detail.geneFunction} (${phageIDsWithNames})`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9844,"value":"function formatFunctionWithAllPhages(detail) {\n const phageIDsWithNames = detail.genes\n .map((gene) => `${gene.phageID.trim()}_${gene.name}`)\n .join(\", \");\n return `${detail.geneFunction} (${phageIDsWithNames})`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2390,"value":"### Data for DNA and Protein Sequences of ORFs in Gaps","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":9776,"value":"phages = getPhameratorData(\n dataset,\n `/phagesbycluster/${selectedCluster}`,\n apiKey\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6953,"value":"$3a","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10962,"value":"getPhageGeneAndGapSequencesFilteredByORF = {\n //Filter the getPhageGeneAndGapSequences by the ORF criteria set by the user.\n //An ORF set to a minumum of 100 will filter getPhageGeneAndGapSequences to include phages with gaps > 100\n const filteredResults = Object.keys(getPhageGeneAndGapSequences).reduce(\n (acc, key) => {\n const item = getPhageGeneAndGapSequences[key];\n // Check if the item contains genes and access the gap value accordingly\n if (item.genes && item.genes[0] && item.genes[0].gap > selectORFLength) {\n acc[key] = item;\n }\n return acc;\n },\n {}\n );\n\n return filteredResults;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9860,"value":"fetchAllPhageData = async (phages, dataset, apiKey) => {\n return await Promise.all(\n phages.map((phage) =>\n getPhameratorData(dataset, `/genome/${phage.phagename}/`, apiKey)\n )\n );\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9862,"value":"reverseString = memoize((str) => str.split(\"\").reverse().join(\"\"))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9867,"value":"// Define complementary and reverse string functions\ncomplementarySequence = memoize((sequence) => {\n const complementMap = { A: \"T\", T: \"A\", C: \"G\", G: \"C\" };\n return sequence\n .split(\"\")\n .map((base) => complementMap[base] || base)\n .join(\"\");\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9869,"value":"// Memoization utility to enhance performance of repetitive function calls\nmemoize = (fn) => {\n const cache = new Map();\n return (...args) => {\n const key = JSON.stringify(args);\n if (cache.has(key)) {\n return cache.get(key);\n } else {\n const result = fn(...args);\n cache.set(key, result);\n return result;\n }\n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7097,"value":"$3b","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10967,"value":"function processStopCodons(sequence, stopCodonList, gene, strand, gapStart) {\n const stopCodons = [];\n for (let i = 0; i < sequence.length - 2; i++) {\n const codon = sequence.substr(i, 3);\n if (stopCodonList.includes(codon)) {\n stopCodons.push({\n stopCodon: codon,\n stopCodonBP: strand === \"FORWARD\" ? gapStart + i + 2 : gapStart + i + 3,\n stopCodonPosition: i,\n geneStrand: strand\n });\n }\n }\n return stopCodons;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7235,"value":"$3c","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9903,"value":"$3d","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7112,"value":"$3e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7491,"value":"//Function to download all gap protein sequences for the phage\nfunction downloadProteinSequences(data) {\n const fileName = filterGeneGapsByPhage + \"_protein_sequences.fasta\";\n // Constructing each sequence in FASTA format\n const text = data\n .map(\n (d) =>\n `>${filterGeneGapsByPhage}_gp${d.Gene}_Start_${d.Start_bp}_Stop_${d.Stop_bp}\\n${d.Protein}`\n )\n .join(\"\\n\");\n const element = document.createElement(\"a\");\n element.setAttribute(\n \"href\",\n \"data:text/plain;charset=utf-8,\" + encodeURIComponent(text)\n );\n element.setAttribute(\"download\", fileName);\n\n element.style.display = \"none\";\n document.body.appendChild(element);\n\n element.click();\n\n document.body.removeChild(element);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7524,"value":"//Function to download all gap protein sequences for the phage\nfunction downloadDNASequences(data) {\n const fileName = filterGeneGapsByPhage + \"_DNA_sequences.fasta\";\n // Constructing each sequence in FASTA format\n const text = data\n .map(\n (d) =>\n `>${filterGeneGapsByPhage}_gp${d.Gene}_Start_${d.Start_bp}_Stop_${d.Stop_bp}\\n${d.DNA}`\n )\n .join(\"\\n\");\n const element = document.createElement(\"a\");\n element.setAttribute(\n \"href\",\n \"data:text/plain;charset=utf-8,\" + encodeURIComponent(text)\n );\n element.setAttribute(\"download\", fileName);\n\n element.style.display = \"none\";\n document.body.appendChild(element);\n\n element.click();\n\n document.body.removeChild(element);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3462,"value":"### Data for Gene Lengths","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":7555,"value":"proteinLengths = phageGenesToHarmonize.map((item) => ({\n phamName: parseInt(item.phamName, 10),\n phageID: item.phageID,\n name: parseInt(item.name, 10),\n genefunction: item.genefunction,\n proteinLength: item.translation.length\n}))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10520,"value":"proteinLengthsAnnotatedPhages = annotatedPhageGenesByCluster.map((item) => ({\n phamName: parseInt(item.phamName, 10),\n phageID: item.phageID,\n name: parseInt(item.name, 10),\n genefunction: item.genefunction,\n proteinLength: item.translation.length\n}))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5145,"value":"$3f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5168,"value":"formattedProteinLengthData = Object.entries(proteinLengthData).map(\n ([phamName, data]) => ({\n phamName: parseInt(phamName, 10),\n genefunction: data.genefunction,\n MaxProteinLength: data.maxProteinLength + \"(\" + data.maxCount + \")\",\n MinProteinLength: data.minProteinLength + \"(\" + data.minCount + \")\",\n Difference: data.maxProteinLength - data.minProteinLength,\n phageCount: data.phageCount,\n UniqueProteinLengths: data.uniqueProteinLengths.size\n })\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10025,"value":"### Data for Gene Gap Analysis","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10027,"value":"$40","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10813,"value":"//Get the number of rows in the GeneLengthAnalysis Inputs.table ... for some reason the count of the table items would only properly update when a user scrolled to the bottom of the table and then manually runs the label code\nrowCountGeneGapAnalysis = {\n const filteredData =\n showPhamGaps === \"Different lengths\"\n ? analyzeGaps.filter((d) => d.PercentCalled !== \"100.00%\")\n : analyzeGaps.filter((d) => d.PercentCalled === \"100.00%\");\n\n // Return the count of rows\n return filteredData.length;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10081,"value":"### Data for Gene Function Analysis","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10079,"value":"$41","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10802,"value":"//Get the number of rows in the GeneLengthAnalysis Inputs.table ... for some reason the count of the table items would only properly update when a user scrolled to the bottom of the table and then manually runs the label code\nrowCounrGeneFunctionAnalysis = {\n const filteredData =\n showPhamFunctions === \"Different functions\"\n ? analyzeFunctions.filter((d) => d.PercentCalled !== \"100.00%\")\n : analyzeFunctions.filter((d) => d.PercentCalled === \"100.00%\");\n\n // Return the count of rows\n return filteredData.length;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10105,"value":"### Data for Gene Length Analysis","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":10107,"value":"$42","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10794,"value":"//Get the number of rows in the GeneLengthAnalysis Inputs.table ... for some reason the count of the table items would only properly update when a user scrolled to the bottom of the table and then manually runs the label code\nrowCountGeneLengthAnalysis = {\n const filteredData =\n showPhamLengths === \"Different lengths\"\n ? analyzeLengths.filter((d) => d.PercentCalled !== \"100.00%\")\n : analyzeLengths.filter((d) => d.PercentCalled === \"100.00%\");\n\n // Return the count of rows\n return filteredData.length;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3128,"value":"### Data for Start Sites Organization","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3531,"value":"$43","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3316,"value":"//Not all phages in the cluster are present in each pham\n//Here we will get a list of all the phams and add all of the phages in the pham\n//Phages without a gene in the pham will have the gene as \"-\"\n//This is to help organize the input of the date to form a grid\n//Explanation could be better - revist this later./KF\nphamWithPhages = {\n const phamWithPhages = {};\n\n phageGenesToHarmonize.forEach(({ phamName, phageID }) => {\n if (!phamWithPhages[phamName]) {\n phamWithPhages[phamName] = new Set();\n }\n phamWithPhages[phamName].add(phageID);\n });\n\n const organizedPhams = Object.entries(phamWithPhages).map(\n ([phamName, phageIDSet]) => {\n return { pham: phamName, phageName: Array.from(phageIDSet) };\n }\n );\n\n return organizedPhams;\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":306,"value":"phageNames = phagesByCluster.map((phageObject) => {\n return phageObject.phagename;\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9984,"value":"$44","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5390,"value":"---\n# Code for Data Download\n---\n### Code to Download Cluster Fasta Files","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":8330,"value":"phagesByCluster_ClusterDNASequenceDownloads = {\n let allPhages = await getPhameratorData(\n dataset,\n `/phagesbycluster/${selectedDataCluster}`,\n apiKey\n );\n\n return showClusterDownload_DraftPhages === \"No\"\n ? allPhages.filter((phage) => !phage.phagename.endsWith(\"_Draft\"))\n : allPhages;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9914,"value":"subclusters_ForPhageDNADownload = {\n const uniqueSubclustersSet =\n phagesByCluster_ClusterDNASequenceDownloads.reduce((subClusters, phage) => {\n subClusters.add(phage.clusterSubcluster);\n return subClusters;\n }, new Set());\n\n // Convert Set to array, sort it alphabetically\n const sortedSubclusters = Array.from(uniqueSubclustersSet).sort();\n\n // Prepend \"All subclusters\" to the sorted array\n sortedSubclusters.unshift(\"All subclusters\");\n return sortedSubclusters;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9912,"value":"phagesByCluster_ClusterDNASequenceDownloads_Filtered = {\n // Immediate return if no specific subcluster is selected\n if (selectedSubcluster_ForPhageDNASequenceDownload === \"All subclusters\") {\n return phagesByCluster_ClusterDNASequenceDownloads;\n }\n\n // Only filter if a specific subcluster is selected\n return phagesByCluster_ClusterDNASequenceDownloads.filter(\n (phage) =>\n phage.clusterSubcluster === selectedSubcluster_ForPhageDNASequenceDownload\n );\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8436,"value":"### Code to Download Pham DNA Sequences or Protein Sequences (.fasta)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":8440,"value":"Show phams in the selected cluster \"selectedDataClusterForPhamDownloads\"","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":5989,"value":"//Updates the selectedDataPham combobox with the Phams in the Cluster selected from the selectedDataCluster combobox\nphamsbyDataCluster = Array.from(\n genesbyDataCluster.reduce((acc, item) => {\n acc.add(item.phamName);\n return acc;\n }, new Set())\n).sort((a, b) => Number(a) - Number(b))\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5641,"value":"phamily = getPhameratorData(\n dataset,\n `/phamily/${selectedDataPham}`,\n apiKey\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6000,"value":"// Get the genes from all phages in the selected cluster for data downloading\ngenesbyDataCluster = await getPhameratorData(\n dataset,\n `/genesbycluster/${selectedDataClusterForPhamDownloads}`,\n apiKey\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9524,"value":"phamData_IncludingOnlyPhagesFromSelectedCluster = {\n const matchingPhams = genesbyDataCluster.filter(\n (gene) => gene.phamName === selectedDataPham\n );\n\n return matchingPhams;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6119,"value":"getPhamProteinSequncesForDownload = {\n let clusterPhages = genesbyDataCluster; // Assuming this function is async and fetches data\n let clusterPhageIDs = clusterPhages.map((p) => p.Phage);\n\n // Filter the phamily array based on the selected radio option\n const filteredPhamily = phamily.filter((item) => {\n // Include item if \"All Pham Genes\" is selected or if it's in the cluster list when \"Cluster Pham Genes Only\" is selected\n return (\n filterPhamDownloadData === \"All Pham Genes\" ||\n clusterPhageIDs.includes(item.phageID)\n );\n });\n\n // Map the filtered phamily data to the required format\n return filteredPhamily.map((item) => ({\n Phage: `${item.phageID}_CDS_${item.name}`,\n Translation: item.translation\n }));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9649,"value":"### Code to create DNA Sequences of Gaps Upstream of a Pham","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":169,"value":"phagesForPhamDownloads = getPhameratorData(\n dataset,\n `/phagesbycluster/${selectedDataClusterForPhamDownloads}`,\n apiKey\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5758,"value":"dataPhages = getPhameratorData(\n dataset,\n `/phagesbycluster/${selectedDataClusterForPhamDownloads}`,\n apiKey\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5896,"value":"phamilies = getPhameratorData(dataset, \"/phamilies\", apiKey)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":297,"value":"genes = {\n let genes = await getPhameratorData(\n dataset,\n `/genesbycluster/${selectedCluster}`,\n apiKey\n );\n\n genes.sort((a, b) => {\n if (a.phageID === b.phageID) {\n return +a.name - +b.name;\n } else {\n return a.phageID < b.phageID ? -1 : 1;\n }\n });\n\n genes = genes.map((gene, index) => {\n const upstreamRightEnd =\n index === 0 || gene.phageID != genes[index - 1].phageID\n ? 1\n : d3.max([+genes[index - 1].start, +genes[index - 1].stop]);\n\n const leftEnd = d3.min([+gene.start, +gene.stop]);\n\n return {\n \"Phage Name\": gene.phageID,\n \"Gene Name\": +gene.name,\n Start: +gene.start,\n Stop: +gene.stop,\n Direction: gene.direction,\n Length: Math.abs(+gene.stop - +gene.start) + 1,\n \"Gap Size\": gene.gap,\n Phamily: +gene.phamName,\n Function: gene.genefunction === \"\" ? \"Unknown\" : gene.genefunction\n };\n });\n\n return genes;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5004,"value":"phamsbycluster = Array.from(\n phageGenesByCluster.reduce((acc, item) => {\n acc.add(item.phamName);\n return acc;\n }, new Set())\n).sort((a, b) => Number(a) - Number(b))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8011,"value":"### Data for Extending Genes","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3460,"value":"getGeneLengthsByPham = {\n const groupedByPhamName = {};\n\n phageGenesByCluster.forEach(\n ({ phamName, phageID, name, start, stop, direction, translation }) => {\n // Calculate genelength based on direction. Forward = stop - start. Else it is reverse = start - stop\n // Could have just did absolute value here\n const genelength = direction === \"forward\" ? stop - start : start - stop;\n\n // Check if this phamName is already a key in the grouped object\n if (!groupedByPhamName[phamName]) {\n groupedByPhamName[phamName] = [];\n }\n\n // Add the processed data to the phamName's array\n groupedByPhamName[phamName].push({\n phamName,\n phageID,\n name,\n genelength,\n translation\n });\n }\n );\n\n // Convert the grouped object into an array format\n return Object.keys(groupedByPhamName).map((phamName) => {\n return { phamName, genes: groupedByPhamName[phamName] };\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1631,"value":"### Data for Cluster-Specific Phamilies","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3113,"value":"getAccessionByPhage = {\n const uniquePairs = phageGenesByCluster.reduce((accumulator, item) => {\n const pairIdentifier = `${item.phageID}_${item.Accession}`;\n if (!accumulator.has(pairIdentifier)) {\n accumulator.set(pairIdentifier, {\n phageID: item.phageID,\n Accession: item.accession\n });\n }\n return accumulator;\n }, new Map());\n\n return Array.from(uniquePairs.values());\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":379,"value":"$45","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5551,"value":"### Code to create an array of DNA Sequences Upstream of a Pham to the stop of the previous gene","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":5582,"value":"$46","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5592,"value":"function downloadPhamGaps() {\n const genes = GetPhageGapSequences[selectedDataPham].genes;\n\n let fastaContent = genes\n .map((gene) => {\n return `>${gene.phagename}_${gene.name}\\n${gene.gapSequence}`;\n })\n .join(\"\\n\");\n\n const blob = new Blob([fastaContent], { type: \"text/plain\" });\n const url = URL.createObjectURL(blob);\n\n const a = document.createElement(\"a\");\n a.href = url;\n a.download = `${selectedDataset}_Pham-${selectedDataPham}_Cluster-${selectedDataClusterForPhamDownloads}.fasta`;\n document.body.appendChild(a);\n a.click();\n document.body.removeChild(a);\n URL.revokeObjectURL(url);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5754,"value":"$47","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6164,"value":"function downloadAllPhamGaps() {\n const genes = GetAllPhageDNASequences[selectedDataPham].genes;\n\n let fastaContent = genes\n .map((gene) => {\n return `>${gene.phagename}_${gene.name}\\n${gene.gapSequence}`;\n })\n .join(\"\\n\");\n\n const blob = new Blob([fastaContent], { type: \"text/plain\" });\n const url = URL.createObjectURL(blob);\n\n const a = document.createElement(\"a\");\n a.href = url;\n a.download = `${selectedDataset}_Pham-${selectedDataPham}_Cluster-${selectedDataClusterForPhamDownloads}.fasta`;\n document.body.appendChild(a);\n a.click();\n document.body.removeChild(a);\n URL.revokeObjectURL(url);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":27,"value":"---\n# Appendix\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":343,"value":"import { gcPlotData, calcGC, revComp } with {\n dataset,\n formData,\n selectedCluster\n} from \"2643c325e269eaed\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11274,"value":"viewof apiKey = {\n const savedKey = localStorage.getItem(\"phamerator_api_key\") || \"\";\n\n const input = Inputs.password({\n label: \"Enter your Phamerator API Key\",\n value: savedKey,\n placeholder: \"Key is saved locally...\"\n });\n\n input.addEventListener(\"input\", () => {\n localStorage.setItem(\"phamerator_api_key\", input.value);\n });\n\n return input;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11300,"value":"getUser = async (apiKey) => {\n let user = await d3.json(`https://classic.phamerator.org/api/profile`, {\n headers: new Headers({\n Authorization: `Bearer ${apiKey}`\n })\n });\n delete user.apiKeys;\n user.password = apiKey;\n return user;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11315,"value":"user = getUser(apiKey)\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11331,"value":"getPhameratorData = async (dataset, endpoint, apiKey) => {\n return await d3.json(\n `https://classic.phamerator.org/api/${dataset}${endpoint}`,\n {\n headers: new Headers({\n Authorization: `Bearer ${apiKey}`\n })\n }\n );\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8947,"value":"\n\n\n\nPhage Gene Analysis\n\n\n\n\n\n\n\n\n","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"}],"files":"$W48","stdlib":"1","titling":"auto"}} 2d:"$2c:body"