28:null 29:["$","title",null,{"children":"BlastN Contig Sequences | WabushOnce | Observable"}] 2e:T477,phagesdbDatabaseStatus = { const detected = phagesdbDatabases?.[0] ?? null; return html`

${ detected ? html` Acinto database version detected : ${detected.label} — ${detected.value} ` : html` Automatic lookup unavailable. Confirm or edit the database version manually. Open the PhagesDB BLAST page or view its source to find the current Acti_######## value. ` }

`; }2f:T636,controlPanel = html`

FASTA Contig Search

${viewof fastaFile}

Contig Length

Min

${viewof minLengthFilter}

Max

${viewof maxLengthFilter}

Contig Number

Min

${viewof minContigNumFilter}

Max

${viewof maxContigNumFilter}

`30:T3d0a,viewof blastTable = { if (!contigsFiltered.length) { return html`

No contigs match the current filters.

`; } let sortColumn = "length"; let sortAsc = false; let pageSize = 20; let currentPage = 1; const selectedIds = new Set(); const ncbiProxyUrl = typeof ncbiBlastProxyUrl === "string" ? ncbiBlastProxyUrl.trim() : ""; const ncbiAvailable = /^https:\/\/.+/i.test(ncbiProxyUrl); const phagesdbValue = typeof phagesdbDatabaseVersion === "string" ? phagesdbDatabaseVersion.trim() : ""; const phagesdbAvailable = /^Acti_\d{8}$/i.test(phagesdbValue); const container = html`

BLAST Results (${contigs.length} contigs total)

${ !ncbiAvailable ? html`

The NCBI BLAST gateway URL is unavailable. NCBI BLASTN submission is disabled, but sequence copying and FASTA downloading remain available.

` : "" } ${ !phagesdbAvailable ? html`

Enter a valid PhagesDB database version to enable PhagesDB BLASTN.

` : "" }

Show rows 0 selected

Select	Contig ID	Length (bp)	NCBI BLASTN	PhagesDB BLASTN	Copy Sequence

`; const tbody = container.querySelector("tbody"); const pageSizeSelect = container.querySelector(".page-size"); const prevButton = container.querySelector(".prev-page"); const nextButton = container.querySelector(".next-page"); const pageInfo = container.querySelector(".page-info"); const downloadButton = container.querySelector(".download-selected"); const selectionCount = container.querySelector(".selection-count"); function getSortedRows() { const rows = contigsFiltered.map((contig) => ({ id: contig.id, idNum: contig.idNum, length: contig.length, sequence: contig.sequence })); rows.sort((a, b) => { const av = a[sortColumn]; const bv = b[sortColumn]; if (sortColumn === "id") { const anum = a.idNum ?? parseInt(String(a.id).match(/\d+$/)?.[0] ?? "0", 10); const bnum = b.idNum ?? parseInt(String(b.id).match(/\d+$/)?.[0] ?? "0", 10); if (anum !== bnum) { return sortAsc ? anum - bnum : bnum - anum; } return sortAsc ? String(a.id).localeCompare(String(b.id)) : String(b.id).localeCompare(String(a.id)); } if (typeof av === "number" && typeof bv === "number") { return sortAsc ? av - bv : bv - av; } if (av < bv) return sortAsc ? -1 : 1; if (av > bv) return sortAsc ? 1 : -1; return 0; }); return rows; } function updateSelectionStatus() { selectionCount.textContent = `${selectedIds.size} selected`; downloadButton.disabled = selectedIds.size === 0; } function createHiddenField(form, name, value, useTextarea = false) { const field = useTextarea ? document.createElement("textarea") : document.createElement("input"); if (!useTextarea) { field.type = "hidden"; } field.style.display = "none"; field.name = name; field.value = value; form.appendChild(field); } function renderTable() { const rows = getSortedRows(); const totalPages = Math.max(1, Math.ceil(rows.length / pageSize)); if (currentPage > totalPages) { currentPage = totalPages; } if (currentPage < 1) { currentPage = 1; } const start = (currentPage - 1) * pageSize; const pageRows = rows.slice(start, start + pageSize); tbody.innerHTML = ""; for (const row of pageRows) { const selectBox = html` `; selectBox.checked = selectedIds.has(row.id); selectBox.onchange = () => { if (selectBox.checked) { selectedIds.add(row.id); } else { selectedIds.delete(row.id); } updateSelectionStatus(); }; /* * NCBI BLASTN * * Sends the complete contig to the Cloudflare Worker. * The Worker submits it to NCBI and returns the BLAST RID URL. */ const blastNcbiButton = html` `; blastNcbiButton.disabled = !ncbiAvailable; blastNcbiButton.title = ncbiAvailable ? "Submit this contig to NCBI BLASTN" : "NCBI BLAST gateway URL is unavailable"; blastNcbiButton.onclick = async () => { if (!ncbiAvailable) { alert("The NCBI BLAST gateway URL is unavailable."); return; } /* * Open a temporary tab immediately so the browser does not * block the results page as a delayed popup. */ const pendingWindow = window.open("about:blank", "_blank"); const originalText = blastNcbiButton.textContent; blastNcbiButton.disabled = true; blastNcbiButton.textContent = "Submitting..."; try { const response = await fetch(ncbiProxyUrl, { method: "POST", headers: { "Content-Type": "application/json" }, body: JSON.stringify({ id: row.id, sequence: row.sequence, program: "blastn", database: "nt", task: "megablast" }) }); let result; try { result = await response.json(); } catch { throw new Error( `The BLAST gateway returned HTTP ${response.status} without a valid JSON response.` ); } if (!response.ok) { const details = result.details ? `\n\n${result.details}` : ""; throw new Error( `${result.error || `HTTP ${response.status}`}${details}` ); } if (!result.resultsUrl) { throw new Error( "The BLAST gateway did not return an NCBI results URL." ); } if (pendingWindow) { pendingWindow.location.href = result.resultsUrl; } else { window.open(result.resultsUrl, "_blank", "noopener,noreferrer"); } blastNcbiButton.textContent = "Submitted"; setTimeout(() => { blastNcbiButton.textContent = originalText; blastNcbiButton.disabled = false; }, 1500); } catch (error) { if (pendingWindow) { pendingWindow.close(); } console.error("NCBI BLAST submission error:", error); alert( `NCBI BLAST submission failed:\n\n${ error instanceof Error ? error.message : String(error) }` ); blastNcbiButton.textContent = originalText; blastNcbiButton.disabled = false; } }; /* * PhagesDB BLASTN */ const phagesButton = html` `; phagesButton.disabled = !phagesdbAvailable; phagesButton.title = phagesdbAvailable ? `Search PhagesDB database ${phagesdbValue}` : "Enter a valid PhagesDB database version"; phagesButton.onclick = () => { if (!phagesdbAvailable) { alert( "Enter the PhagesDB database version as Acti_MMDDYYYY, for example Acti_08032026." ); return; } const fastaText = `>${row.id}\n${wrapSequence(row.sequence)}`; const form = document.createElement("form"); form.method = "POST"; form.target = "_blank"; form.action = phagesdbBlastUrl; createHiddenField(form, sequenceFieldName, fastaText, true); createHiddenField(form, "PROGRAM", "blastn"); createHiddenField(form, "DATALIB", phagesdbValue); createHiddenField(form, "ALIGNMENT_VIEW", "0"); createHiddenField(form, "OVERVIEW", "on"); document.body.appendChild(form); form.submit(); setTimeout(() => { form.remove(); }, 1000); }; /* * Copy sequence */ const copyButton = html` `; copyButton.onclick = async () => { try { await navigator.clipboard.writeText(row.sequence); copyButton.textContent = "Copied"; setTimeout(() => { copyButton.textContent = "Copy"; }, 1000); } catch (error) { console.error("Clipboard error:", error); copyButton.textContent = "Error"; setTimeout(() => { copyButton.textContent = "Copy"; }, 1500); } }; tbody.append(html` ${selectBox} ${row.id} ${row.length.toLocaleString()} ${blastNcbiButton} ${phagesButton} ${copyButton} `); } pageInfo.textContent = `Page ${currentPage} of ${totalPages}`; prevButton.disabled = currentPage === 1; nextButton.disabled = currentPage === totalPages; updateSelectionStatus(); } pageSizeSelect.onchange = () => { pageSize = Number(pageSizeSelect.value); currentPage = 1; renderTable(); }; prevButton.onclick = () => { if (currentPage > 1) { currentPage -= 1; renderTable(); } }; nextButton.onclick = () => { const totalPages = Math.max( 1, Math.ceil(getSortedRows().length / pageSize) ); if (currentPage < totalPages) { currentPage += 1; renderTable(); } }; downloadButton.onclick = () => { const selectedRows = getSortedRows().filter((row) => selectedIds.has(row.id) ); if (!selectedRows.length) { return; } const fastaText = selectedRows .map((row) => `>${row.id}\n${wrapSequence(row.sequence)}`) .join("\n"); const blob = new Blob([fastaText], { type: "text/plain;charset=utf-8" }); const url = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = url; link.download = "selected_contigs.fasta"; document.body.appendChild(link); link.click(); document.body.removeChild(link); setTimeout(() => { URL.revokeObjectURL(url); }, 0); }; for (const header of container.querySelectorAll("th[data-col]")) { header.onclick = () => { const column = header.getAttribute("data-col"); if (sortColumn === column) { sortAsc = !sortAsc; } else { sortColumn = column; sortAsc = column !== "length"; } currentPage = 1; renderTable(); }; } renderTable(); return container; }31:Td44,viewof fastaOutput = { const container = html`

`; const sortLabel = html`Sort reads by:`; const sortSelect = html``; const button = html``; const progress = html``; const status = html`

`; const downloadLink = html``; button.onclick = async () => { if (!fastqFile) { status.textContent = "Please select a FASTQ file first."; downloadLink.style.display = "none"; progress.style.display = "none"; return; } // Show progress bar progress.style.display = "block"; progress.value = 0; status.textContent = "Reading file..."; const text = await fastqFile.text(); status.textContent = "Parsing reads..."; const lines = text.split(/\r?\n/); const n = lines.length; const records = []; // store cleaned sequences in original order let i = 0; while (i < n) { const line = lines[i]; if (line && line.startsWith("@")) { const seqLine = lines[i + 1] || ""; const cleanSeq = seqLine.toUpperCase().replace(/[^ACGTN]/g, ""); if (cleanSeq.length > 0) { records.push(cleanSeq); } i += 4; } else { i += 1; } // Update progress periodically if (i % 4000 === 0 || i >= n) { const pct = Math.round((i / n) * 100); progress.value = pct; status.textContent = `Parsing reads... ${pct}%`; await new Promise(requestAnimationFrame); } } if (!records.length) { status.textContent = "Done – no valid cleaned sequences found."; downloadLink.style.display = "none"; progress.style.display = "none"; return; } // 🔀 Apply sorting based on user choice let sortedRecords; const mode = sortSelect.value; if (mode === "length") { sortedRecords = [...records].sort((a, b) => b.length - a.length); } else { // "contig" – original order sortedRecords = records; } const fastaLines = []; sortedRecords.forEach((seq, idx) => { fastaLines.push(`>conti_${idx + 1}`); fastaLines.push(seq); }); const fasta = fastaLines.join("\n"); const baseName = fastqFile.name.replace(/\.(fastq|fq|txt)$/i, ""); const fastaFileName = `${baseName}.fasta`; const blob = new Blob([fasta], { type: "text/plain" }); const url = URL.createObjectURL(blob); downloadLink.href = url; downloadLink.download = fastaFileName; downloadLink.textContent = `Download ${fastaFileName}`; downloadLink.style.display = "inline"; progress.value = 100; const modeLabel = mode === "length" ? "read length (longest first)" : "contig order"; status.textContent = `Done – ${sortedRecords.length.toLocaleString()} reads written to FASTA (${modeLabel}).`; }; container.append( sortLabel, sortSelect, button, progress, status, downloadLink ); return container; }32:[{"id":"6aa93a5f07b3a763e45ab3f12632d2b7ba434caaec98cc3a692105c34ead4fba7c034ee110505d7d99713b5105718bc6c89874e550551dd0ea2dcc817876fd87","href":"https://static.observableusercontent.com/files/6aa93a5f07b3a763e45ab3f12632d2b7ba434caaec98cc3a692105c34ead4fba7c034ee110505d7d99713b5105718bc6c89874e550551dd0ea2dcc817876fd87","name":"image.png","type":"image/png","lastModified":1776169627803.602,"size":19658},{"id":"193e349e0d84833c401a94aa81ed826057ac293532149d27ba1826e3ef5a351fa2b2bf6fb2e1d1a25e9ebbccb2741c82137a3e4eed9325bd0d5ba05a24badf72","href":"https://static.observableusercontent.com/files/193e349e0d84833c401a94aa81ed826057ac293532149d27ba1826e3ef5a351fa2b2bf6fb2e1d1a25e9ebbccb2741c82137a3e4eed9325bd0d5ba05a24badf72","name":"image@1.png","type":"image/png","lastModified":1776169691958.33,"size":6764}] 2c:{"id":"0c8c71f50dfae923","slug":"blast","title":"BlastN Contig Sequences","thumbnail":"a7322cee04b13d1c8ceb6da83a5e2cfd9805ed1f8408f0bc9e6d1c32369f77ec","access_level":"public","create_time":"$D2025-11-22T20:39:36.881Z","update_time":"$D2026-08-04T17:48:59.403Z","view_time":null,"first_public_time":"$D2025-11-23T02:38:53.980Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"d1dfc5f860fb8699","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":"starter_2024"},"version":767,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"3035ce62f81ebcd9","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":null}],"members":[{"type":"individual","id":"3035ce62f81ebcd9","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":null,"role":"editor"},{"type":"team","id":"d1dfc5f860fb8699","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":true,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"BlastN Contig Sequences","cells":[{"id":0,"value":"# BlastN Contig Sequences\n- Shows each FASTA contig in a table\n- Provides buttons to run a BLASTN search (NCBI or PhagesDB) for each contig.\n- Download selected contigs as a FASTA file.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":704,"value":"$2e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":605,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":736,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":280,"value":"---\n# No contigs from your assembly? No problem.\nYou can still try identifying the phage cluster by running BLASTN on the longest read from your FASTQ file.\n- Convert the FASTQ file to FASTA (removes quality scores) using the script below.\n- Upload the FASTA file to the BLASTN Contig script above.\n- Sort by read length and run BLASTN on the longest reads.\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":285,"value":"viewof fastqFile = Inputs.file({\n label: \"FASTQ file\",\n accept: \".fastq,.fq,.txt\",\n multiple: false\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":302,"value":"readSummary = {\n if (!fastqFile) return \"No file selected.\";\n\n const records = await parseFastqFile(fastqFile);\n const totalReads = records.length;\n\n let totalBases = 0;\n let minLen = Infinity;\n let maxLen = 0;\n\n for (const r of records) {\n const len = r.length; // cleaned length (ACGTN only)\n totalBases += len;\n if (len < minLen) minLen = len;\n if (len > maxLen) maxLen = len;\n }\n\n // Handle edge case: no reads\n if (!totalReads) {\n return html`

\n Reads in file: 0
\n Total bases: 0
\n Read length range: n/a\n

`;\n }\n\n return html`

\n - Reads in file: ${totalReads.toLocaleString()}
\n - Total bases: ${totalBases.toLocaleString()}
\n - Read length range: \n ${minLen.toLocaleString()} bp – \n ${maxLen.toLocaleString()} bp\n

`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":290,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":187,"value":"---\n# Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":465,"value":"## Controls","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":149,"value":"viewof maxLengthFilter = Inputs.number({\n value: 0,\n min: 0,\n step: 100\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":80,"value":"viewof fastaFile = Inputs.file({\n label: \"Select a FASTA file\",\n accept: \".fasta,.fa,.fna,.txt\",\n multiple: false\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":146,"value":"viewof minLengthFilter = Inputs.number({\n value: 0,\n min: 0,\n step: 100\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":152,"value":"viewof minContigNumFilter = Inputs.number({\n value: 0,\n min: 0,\n step: 1\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":155,"value":"viewof maxContigNumFilter = Inputs.number({\n value: 0,\n min: 0,\n step: 1\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":381,"value":"## Code to Blast Contig Sequences","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":657,"value":"#### Open & parse FASTA file.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":112,"value":"// Helper to wrap sequences nicely for FASTA\nfunction wrapSequence(seq, width = 60) {\n const lines = [];\n for (let i = 0; i < seq.length; i += width) {\n lines.push(seq.slice(i, i + width));\n }\n return lines.join(\"\\n\");\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":73,"value":"function parseFasta(lines) {\n const records = [];\n let header = null;\n let seqParts = [];\n\n for (const line of lines) {\n if (!line.trim()) continue;\n\n if (line.startsWith(\">\")) {\n if (header !== null) {\n records.push({\n header,\n id: header.split(/\\s+/)[0].replace(/^>/, \"\"),\n sequence: seqParts.join(\"\")\n });\n }\n header = line;\n seqParts = [];\n } else {\n seqParts.push(line.trim());\n }\n }\n\n if (header !== null) {\n records.push({\n header,\n id: header.split(/\\s+/)[0].replace(/^>/, \"\"),\n sequence: seqParts.join(\"\")\n });\n }\n\n return records;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":95,"value":"fastaArrayBuffer = fastaFile ? await fastaFile.arrayBuffer() : null\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":180,"value":"fastaLines = fastaArrayBuffer\n ? new TextDecoder().decode(new Uint8Array(fastaArrayBuffer)).split(/\\r?\\n/)\n : []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":162,"value":"// Store text inside an object so Observable doesn't try to render the full sequence\nfastaTextObj = fastaArrayBuffer\n ? { text: new TextDecoder().decode(new Uint8Array(fastaArrayBuffer)) }\n : null","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":64,"value":"contigs = fastaLines.length ? parseFasta(fastaLines) : []","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":166,"value":"contigsFiltered = {\n const minLen = minLengthFilter || 0;\n const maxLen = maxLengthFilter || 0;\n const minNum = minContigNumFilter || 0;\n const maxNum = maxContigNumFilter || 0;\n\n return contigs\n .map((c) => {\n const idNum = parseInt(String(c.id).match(/\\d+$/)?.[0] ?? 0, 10);\n return {\n ...c,\n idNum,\n length: c.sequence.length\n };\n })\n .filter((r) => {\n if (minLen > 0 && r.length < minLen) return false;\n if (maxLen > 0 && r.length > maxLen) return false;\n if (minNum > 0 && r.idNum < minNum) return false;\n if (maxNum > 0 && r.idNum > maxNum) return false;\n return true;\n });\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":204,"value":"// PhagesDB BLAST endpoint and sequence field name\nphagesdbBlastUrl = \"https://phagesdb.org/blast/results/blast.cgi\";","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":207,"value":"sequenceFieldName = \"SEQUENCE\"\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":647,"value":"#### Get and parse \"phagesdb.org/blast\" source code to get PhagesDB version ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":527,"value":"phagesdbDatabases = {\n try {\n const response = await fetch(\n `${ncbiBlastProxyUrl.replace(/\\/+$/, \"\")}/phagesdb-version`,\n {\n cache: \"no-store\"\n }\n );\n\n const result = await response.json();\n\n if (!response.ok || result.status !== \"ok\" || !result.database?.value) {\n throw new Error(result.error || \"PhagesDB database lookup failed.\");\n }\n\n return [\n {\n label: result.database.label,\n value: result.database.value,\n automatic: true\n }\n ];\n } catch (error) {\n console.warn(\"Automatic PhagesDB database lookup failed:\", error);\n\n return [];\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":535,"value":"phagesdbActinoDatabase = phagesdbDatabases.find((d) =>\n d.value.startsWith(\"Acti_\")\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":212,"value":"viewof phagesdbProgram = Inputs.select([\"blastn\", \"tblastn\", \"tblastx\"], {\n label: \"PhagesDB program (PROGRAM)\",\n value: \"blastn\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":707,"value":"viewof phagesdbDatabaseVersion = Inputs.text({\n label: \"PhagesDB database version\",\n value: phagesdbDatabases?.[0]?.value ?? \"Acti_08032026\",\n placeholder: \"Acti_MMDDYYYY\",\n width: 300\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":299,"value":"## Code to Convert .FastQ to .FastA","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":282,"value":"// 2. Helper to convert FASTQ text to cleaned FASTA\nfunction fastqToCleanFasta(text) {\n const lines = text.split(/\\r?\\n/);\n const fastaLines = [];\n let i = 0;\n let contigIndex = 0;\n\n while (i < lines.length) {\n const line = lines[i];\n\n // Detect FASTQ header line\n if (line && line.startsWith(\"@\")) {\n const seqLine = lines[i + 1] || \"\";\n const cleanSeq = seqLine.toUpperCase().replace(/[^ACGTN]/g, \"\"); // keep only A C G T N\n\n if (cleanSeq.length > 0) {\n contigIndex += 1;\n fastaLines.push(`>contig_${contigIndex}`);\n fastaLines.push(cleanSeq);\n }\n\n // Skip to next FASTQ record (4-line blocks)\n i += 4;\n } else {\n i += 1;\n }\n }\n\n return fastaLines.join(\"\\n\");\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":287,"value":"import { Inputs } from \"@observablehq/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":304,"value":"async function parseFastqFile(file) {\n const text = await file.text();\n const lines = text.split(/\\r?\\n/);\n const records = [];\n\n let i = 0;\n while (i < lines.length) {\n const line = lines[i];\n\n if (line && line.startsWith(\"@\")) {\n const seqLine = lines[i + 1] || \"\";\n const cleanSeq = seqLine.toUpperCase().replace(/[^ACGTN]/g, \"\");\n\n records.push({\n index: records.length + 1,\n cleanSeq,\n length: cleanSeq.length\n });\n\n i += 4;\n } else {\n i += 1;\n }\n }\n\n return records;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":732,"value":"ncbiBlastProxyUrl = \"https://observable-ncbi-blast.wabushonce.workers.dev\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":734,"value":"ncbiBlastEmail = \"wabushonce@gmail.com\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W32","stdlib":"1","titling":"auto"}} 2d:"$2c:body"