GFF and GFF3 File Parser

27:null 28:["$","title",null,{"children":"RIME vs. Manual Annotations | WabushOnce | Observable"}] 2d:T6c6, GFF and GFF3 File Parser

.gff File Data

ID	Product	Start	Stop	Direction	Inference	Organism	Insert	Delete

.gff3 File Data

ID	Product	Start	Stop	Direction	Insert	Delete

2e:T4d2,function generateStatisticsTable() { const gffTable = document.getElementById('gffTable'); const gff3Table = document.getElementById('gff3Table'); const statsTable = document.createElement('table'); statsTable.border = '1'; document.body.appendChild(statsTable); const headerRow = statsTable.insertRow(); ['Column', 'Matches', 'Differences'].forEach(text => { const cell = headerRow.insertCell(); cell.textContent = text; }); const columnsToCompare = [1, 2, 3]; // Indexes of Product, Start, Stop columns const columnNames = ['Product', 'Start', 'Stop']; columnsToCompare.forEach((index, colIndex) => { const row = statsTable.insertRow(); row.insertCell().textContent = columnNames[colIndex]; let matches = 0, differences = 0; for (let i = 1; i < Math.min(gffTable.rows.length, gff3Table.rows.length); i++) { if (gffTable.rows[i].cells[index].textContent === gff3Table.rows[i].cells[index].textContent) { matches++; } else { differences++; } } row.insertCell().textContent = matches; row.insertCell().textContent = differences; }); }2f:[] 2b:{"id":"5c80e627f2dd1521","slug":null,"title":"RIME vs. Manual 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vs. Manual Annotations","cells":[{"id":0,"value":"# RIME vs. Manual Annotations ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":60,"value":"---\n## Select RIME (.gff) and Manual (.gff3) genome annotation files to be parsed.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":96,"value":"$2d","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":152,"value":"\n","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":175,"value":"document.getElementById(\"compareTables\").addEventListener(\"click\", function () {\n compareTables();\n generateStatisticsTable();\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":16,"value":"---\n# Coding","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":18,"value":"document\n .getElementById(\"fileInput\")\n .addEventListener(\"change\", function (event) {\n const file = event.target.files[0];\n const fileType = file.name.split(\".\").pop().toLowerCase();\n const reader = new FileReader();\n\n reader.onload = function (e) {\n const lines = e.target.result.split(\"\\n\");\n const gffTable = document.getElementById(\"gffTable\");\n const gff3Table = document.getElementById(\"gff3Table\");\n\n if (fileType === \"gff\") {\n clearTable(gffTable);\n processFile(lines, gffTable, parseGff);\n } else if (fileType === \"gff3\") {\n clearTable(gff3Table);\n processFile(lines, gff3Table, parseGff3);\n }\n };\n\n reader.readAsText(file);\n })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":221,"value":"function extractTableData(table) {\n return Array.from(table.rows)\n .slice(1)\n .map(function (row) {\n return Array.from(row.cells).map(function (cell) {\n return cell.textContent;\n });\n });\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":146,"value":"document.getElementById(\"saveGffData\").addEventListener(\"click\", function () {\n saveData(\"gffTable\");\n alert(\"This is a message!\");\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":80,"value":"document.getElementById(\"saveGff3Data\").addEventListener(\"click\", function () {\n saveData(\"gff3Table\");\n alert(\"This is a message!\");\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":102,"value":"document.getElementById(\"compareTables\").addEventListener(\"click\", function () {\n compareTables();\n generateStatisticsTable();\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":78,"value":"function processFile(lines, table, parserFunc) {\n lines.forEach((line) => {\n if (line.startsWith(\"#\") || line.trim() === \"\") return;\n const fields = line.split(\"\\t\");\n if (fields.length < 9) return;\n parserFunc(fields, table);\n });\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":23,"value":"function parseGff(fields, table) {\n const id = fields[8].split(\";\")[0].split(\"=\")[1];\n const product = fields[8].split(\";\")[1].split(\"=\")[1];\n const start = fields[3];\n const stop = fields[4];\n const direction = fields[6] === \"+\" ? \"forward\" : \"reverse\";\n\n // Extracting the inference data\n let inference = \"\";\n let organism = \"\";\n const attributes = fields[8].split(\";\");\n for (let attr of attributes) {\n if (attr.startsWith(\"inference=\")) {\n inference = attr.split(\"=\")[1];\n } else if (attr.startsWith(\"organism=\")) {\n organism = attr.split(\"=\")[1];\n }\n }\n\n addRow(\n table,\n fields[8].split(\";\")[0].split(\"=\")[1],\n fields[8].split(\";\")[1].split(\"=\")[1],\n fields[3],\n fields[4],\n fields[6] === \"+\" ? \"forward\" : \"reverse\",\n inference,\n organism\n );\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":25,"value":"function parseGff3(fields, table) {\n if (fields[2] !== 'CDS') return;\n const geneValue = fields[8].match(/;gene=([^;]+)/);\n const id = geneValue ? geneValue[1] : '';\n const productMatch = fields[8].match(/;product=([^;]+)/);\n const product = productMatch ? productMatch[1] : '';\n addRow(table, id, product, fields[3], fields[4], fields[6] === '+' ? 'forward' : 'reverse');\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":125,"value":"function addRow(table, id, product, start, stop, direction, inference, organism) {\n const row = table.insertRow();\n [id, product, start, stop, direction, inference, organism].forEach(text => {\n const cell = row.insertCell();\n cell.textContent = text;\n cell.setAttribute('contenteditable', 'true');\n });\n addInsertRowButton(table, row, row.insertCell());\n addDeleteButton(row, row.insertCell());\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":130,"value":"\nfunction addInsertRowButton(table, row, cell) {\n const insertButton = document.createElement('button');\n insertButton.textContent = 'Insert';\n insertButton.addEventListener('click', function() {\n const newRow = table.insertRow(row.rowIndex);\n for (let i = 0; i < row.cells.length - 2; i++) {\n const cell = newRow.insertCell();\n cell.setAttribute('contenteditable', 'true');\n }\n addInsertRowButton(table, newRow, newRow.insertCell());\n addDeleteButton(newRow, newRow.insertCell());\n });\n cell.appendChild(insertButton);\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":141,"value":"\nfunction addDeleteButton(row, cell) {\n const deleteButton = document.createElement('button');\n deleteButton.textContent = 'Delete';\n deleteButton.addEventListener('click', function() {\n row.parentElement.removeChild(row);\n });\n cell.appendChild(deleteButton);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":143,"value":"function saveData(tableId) {\n const table = document.getElementById(tableId);\n let csvContent = \"data:text/csv;charset=utf-8,\";\n\n // Header\n let headerRow = [];\n for (let j = 0; j < table.rows[0].cells.length; j++) {\n headerRow.push(table.rows[0].cells[j].textContent.trim());\n }\n csvContent += headerRow.join(\",\") + \"\\r\\n\";\n\n // Rows\n for (let i = 1; i < table.rows.length; i++) {\n let row = table.rows[i];\n let rowData = [];\n for (let j = 0; j < row.cells.length; j++) {\n rowData.push(row.cells[j].textContent.trim());\n }\n csvContent += rowData.join(\",\") + \"\\r\\n\";\n }\n\n // Download\n var encodedUri = encodeURI(csvContent);\n var link = document.createElement(\"a\");\n link.setAttribute(\"href\", encodedUri);\n link.setAttribute(\"download\", tableId + \".csv\");\n document.body.appendChild(link); // Required for FF\n\n link.click(); // Trigger download\n\n document.body.removeChild(link); // Clean up\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":155,"value":"function clearTable(table) {\n while (table.rows.length > 1) {\n table.deleteRow(1);\n }\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":157,"value":"function compareTables() {\n const gffTable = document.getElementById('gffTable');\n const gff3Table = document.getElementById('gff3Table');\n \n const rowCount = Math.min(gffTable.rows.length, gff3Table.rows.length);\n\n for (let i = 1; i < rowCount; i++) {\n compareRow(gffTable.rows[i], gff3Table.rows[i]);\n }\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":202,"value":"function compareRow(row1, row2) {\n // Assuming the order of columns: ID, Product, Start, Stop, Direction\n const columnsToCompare = [1, 2, 3, 4]; // Indexes of Product, Start, Stop, Direction columns\n\n columnsToCompare.forEach(index => {\n const cellText1 = row1.cells[index].textContent.toLowerCase();\n const cellText2 = row2.cells[index].textContent.toLowerCase();\n\n if (cellText1 === cellText2) {\n row1.cells[index].style.backgroundColor = 'lightgreen';\n row2.cells[index].style.backgroundColor = 'lightgreen';\n } else {\n row1.cells[index].style.backgroundColor = 'yellow';\n row2.cells[index].style.backgroundColor = 'yellow';\n }\n });\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":189,"value":"function extractColumnData(table, columnIndex) {\n return Array.from(table.rows).slice(1).map(row => row.cells[columnIndex].textContent);\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":191,"value":"function addMissingRow(table, stopValue) {\n const row = table.insertRow();\n row.insertCell().textContent = 'missing'; // ID cell\n row.insertCell(); // Product cell\n row.insertCell(); // Start cell\n row.insertCell().textContent = stopValue; // Stop cell\n row.insertCell(); // Direction cell\n addInsertRowButton(table, row, row.insertCell());\n addDeleteButton(row, row.insertCell());\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":193,"value":"\nfunction copyRowToTable(table, rowData) {\n const row = table.insertRow();\n rowData.forEach(cellData => {\n const cell = row.insertCell();\n cell.textContent = cellData;\n });\n addInsertRowButton(table, row, row.insertCell());\n addDeleteButton(row, row.insertCell());\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":197,"value":"$2e","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":213,"value":"function addEmptyRow(table, idValue, stopValue) {\n var row = table.insertRow();\n var idCell = row.insertCell();\n var productCell = row.insertCell();\n var startCell = row.insertCell();\n var stopCell = row.insertCell();\n var directionCell = row.insertCell();\n\n idCell.textContent = idValue;\n stopCell.textContent = stopValue;\n\n // Add editable attribute if needed\n [productCell, startCell, directionCell].forEach(function(cell) {\n cell.setAttribute('contenteditable', 'true');\n });\n\n addInsertRowButton(table, row, row.insertCell());\n addDeleteButton(row, row.insertCell());\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":329,"value":"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":334,"value":"document.addEventListener('DOMContentLoaded', function() {\nconst saveButton = document.getElementById('saveData');\n\n if (saveButton) {\n saveButton.addEventListener('click', function() {\n const table = document.getElementById('resultTable');\n const data = [];\n\n if (table) {\n for (let i = 1; i < table.rows.length; i++) {\n const row = table.rows[i];\n data.push({\n id: row.cells[0].textContent,\n product: row.cells[1].textContent,\n start: row.cells[2].textContent,\n stop: row.cells[3].textContent,\n direction: row.cells[4].textContent\n });\n }\n }\n\n console.log(data); // For demonstration, data is logged to console. Implement saving functionality as needed.\n });\n } else {\n console.error('Save button not found');\n }\n});\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":377,"value":"function addTableToWorkbook(tableId, wb, sheetName) {\n const table = document.getElementById(tableId);\n const ws = XLSX.utils.table_to_sheet(table, { raw: true });\n\n // Apply styles, if any\n for (let i = 1; i < table.rows.length; i++) {\n for (let j = 0; j < table.rows[i].cells.length; j++) {\n const cell = table.rows[i].cells[j];\n const cellRef = XLSX.utils.encode_cell({ c: j, r: i });\n\n if (!ws[cellRef]) ws[cellRef] = {};\n if (cell.style.backgroundColor) {\n if (!ws[cellRef].s) ws[cellRef].s = {};\n ws[cellRef].s.fill = {\n fgColor: { rgb: convertToExcelColor(cell.style.backgroundColor) }\n };\n }\n }\n }\n\n XLSX.utils.book_append_sheet(wb, ws, sheetName);\n}\n\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":380,"value":"function convertToExcelColor(htmlColor) {\n return \"FF\" + htmlColor.slice(1);\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":388,"value":"document.addEventListener('DOMContentLoaded', function() {\n // Your script that uses XLSX\n});","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":360,"value":"\n","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"}],"files":"$W2f","stdlib":"1","titling":"auto"}} 2c:"$2b:body"