Created
November 27, 2022 19:07
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Example of uploading and parsing a GBK file with Pyodide + Biopython
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| <!DOCTYPE html> | |
| <html> | |
| <head> | |
| <script src="https://cdn.jsdelivr.net/pyodide/v0.21.3/full/pyodide.js"></script> | |
| </head> | |
| <body> | |
| Pyodide test page <br> | |
| Open your browser console to see Pyodide output | |
| <p>You can execute any Python code. Just enter something in the box below and click the button.</p> | |
| <input id='code' value='sum([1, 2, 3, 4, 5])'> | |
| <button onclick='evaluatePython()'>Run</button> | |
| <br> | |
| <div> Output: </div> | |
| <textarea id='output' style='width: 100%;' rows='6' disabled></textarea> <br> | |
| <h2> Upload GB | |
| K File Here </h2> | |
| <input type="file" onchange="previewFile()" /><br /> | |
| <p class="content"></p> | |
| <script type="text/javascript"> | |
| // global data | |
| let pyodide; | |
| let gbk_string; | |
| let gbk_pyobj; | |
| let gbk_genes_gaps; | |
| let parse_gbk_string; | |
| const output = document.getElementById("output"); | |
| const code = document.getElementById("code"); | |
| function addToOutput(s) { | |
| output.value += '>>>' + code.value + '\n' + s + '\n'; | |
| } | |
| output.value = 'Initializing...\n'; | |
| function evaluatePython() { | |
| pyodide.runPythonAsync(code.value) | |
| .then(output => addToOutput(output)) | |
| .catch((err) => { addToOutput(err) }); | |
| } | |
| // Load the file and save the parsed file as a global variable | |
| function previewFile() { | |
| const content = document.querySelector('.content'); | |
| const [file] = document.querySelector('input[type=file]').files; | |
| const reader = new FileReader(); | |
| reader.addEventListener("load", () => { | |
| // this will then display a text file | |
| content.innerText = reader.result; | |
| gbk_string = reader.result; | |
| gbk = parse_gbk_string(gbk_string) | |
| gbk_genes_gaps = gbk.toJs() // pyproxy conversion | |
| }, false); | |
| if (file) { | |
| reader.readAsText(file); | |
| } | |
| } | |
| async function main() { | |
| pyodide = await loadPyodide(); | |
| await pyodide.loadPackage("biopython"); | |
| // register a function that will parse input text as a Biopython object. | |
| pyodide.runPython(` | |
| from io import StringIO | |
| from Bio import SeqIO | |
| def parse_gbk_string(genbank_string): | |
| gbk = SeqIO.read(StringIO(genbank_string), format="genbank") | |
| return gbk | |
| `) | |
| // declare global functions | |
| parse_gbk_string = pyodide.globals.get('parse_gbk_string') | |
| }; | |
| main(); | |
| </script> | |
| </body> | |
| </html> |
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