Notebooks 2.0 is here.
Public
Edited
Jul 29
viewof combineAssemblyScript2 = {
const inputPath = Inputs.text({
label: "📂 Path to folder containing barcode directories",
placeholder:
"C:\\Users\\yourname\\Desktop\\Nanopore_Results\\Run1\\Sample1\\assemblies",
style: "width: 600px"
});
const textarea = html`<textarea readonly rows="30" style="width: 100%; font-family: monospace; white-space: pre;"></textarea>`;
const copyButton = html`<button style="padding: 4px 8px; font-size: 0.85em;">📋 Copy</button>`;
copyButton.onclick = () => {
navigator.clipboard.writeText(textarea.value);
copyButton.textContent = "✅ Copied!";
setTimeout(() => (copyButton.textContent = "📋 Copy"), 1500);
};
function toWSLPath(path) {
return path
.replace(/^([A-Za-z]):/, (_, d) => `/mnt/${d.toLowerCase()}`)
.replace(/\\/g, "/");
}
function generateScript() {
const rawPath = inputPath.value.trim();
const path = toWSLPath(rawPath);
textarea.value = `#!/bin/bash
# 🧬 Activate reads-assembly-core environment
source ~/miniconda/etc/profile.d/conda.sh
conda activate reads-assembly-core
# 📁 Define the base directory
base_dir="${path}"
# 📄 Output file for selected data
output_file="\${base_dir}/assembly_summary.tsv"
# 🧾 Write header
echo -e "Barcode\\tseq_name\\tlength\\tcov." > "\${output_file}"
# 🔁 Loop through barcode folders
for dir in "\${base_dir}"/barcode*/; do
folder_name=$(basename "\${dir}")
info_file="\${dir}assembly_info.txt"
if [[ -f "\${info_file}" ]]; then
data_line=$(sed -n '2p' "\${info_file}")
if [[ -n "\${data_line}" ]]; then
seq_name=$(echo "\${data_line}" | cut -f1)
length=$(echo "\${data_line}" | cut -f2)
cov=\$(echo "\${data_line}" | cut -f3)
echo -e "\${folder_name}\\t\${seq_name}\\t\${length}\\t\${cov}" >> "\${output_file}"
fi
else
echo "Warning: Missing \${info_file}"
fi
done
# 📊 Convert to Excel
python3 - <<EOF
import pandas as pd
import os
tsv_path = os.path.join("${path}", "assembly_summary.tsv")
xlsx_path = os.path.join("${path}", "assembly_summary.xlsx")
df = pd.read_csv(tsv_path, sep="\\t")
df.to_excel(xlsx_path, index=False)
EOF
echo "✅ Done! TSV and Excel saved in: \${base_dir}"`;
}
inputPath.addEventListener("input", generateScript);
generateScript();
const controlsPanel = html`<div style="display: flex; flex-direction: column; gap: 1em; min-width: 320px;">
${inputPath}
</div>`;
const outputPanel = html`<div style="flex-grow: 1; display: flex; flex-direction: column; gap: 0.5em;">
${textarea}
${copyButton}
</div>`;
return html`<div style="display: flex; flex-direction: row; gap: 2em; align-items: flex-start;">
${controlsPanel}
${outputPanel}
</div>`;
}
viewof doradoBasecallScript2 = {
const kitInput = Inputs.select(
[
"SQK-RPB114-24",
"EXP-NBD114",
"SQK-PCB109",
"SQK-RAB201",
"Custom-Barcodes"
],
{ label: "🧬 Kit name", value: "SQK-RPB114-24", style: "width: 250px" }
);
const modelInput = Inputs.text({
label: "📈 Model",
value: "sup@v5.2",
style: "width: 250px"
});
const qscoreInput = Inputs.range([0, 30], {
label: "🎯 Minimum Q-score",
value: 10,
step: 1
});
const pod5FolderInput = Inputs.text({
label: "📁 Folder of Pod5 files (Windows path)",
placeholder: "C:\\Users\\YourName\\Desktop\\Nanopore_Data\\Pod5_Files",
style: "width: 600px"
});
const outputPathInput = Inputs.text({
label: "📄 Output BAM file name",
placeholder: "Dorado_Output.bam",
value: "Dorado_Output.bam",
style: "width: 600px"
});
const barcodeArrangementInput = Inputs.text({
label: "🧬 Barcode arrangement TOML (Windows path, optional)",
placeholder: "C:\\Path\\To\\Your\\M13-arrangement.toml",
style: "width: 600px"
});
const barcodeSequencesInput = Inputs.text({
label: "🧬 Barcode sequences FASTA (Windows path, optional)",
placeholder: "C:\\Path\\To\\Your\\barcodes.fasta",
style: "width: 600px"
});
const textarea = html`<textarea readonly rows="10" style="width: 100%; font-family: monospace; white-space: pre;"></textarea>`;
const copyButton = html`<button style="padding: 4px 8px; font-size: 0.9em;">📋 Copy Command</button>`;
function toWSLPath(winPath) {
return winPath
.replace(/^([A-Za-z]):/, (_, d) => `/mnt/${d.toLowerCase()}`)
.replace(/\\/g, "/");
}
function updateScript() {
const pod5WinPath = pod5FolderInput.value.trim();
const outputBam = outputPathInput.value.trim() || "Dorado_Output.bam";
const barcodeToml = barcodeArrangementInput.value.trim();
const barcodeFasta = barcodeSequencesInput.value.trim();
if (!pod5WinPath) {
textarea.value = "";
copyButton.disabled = true;
return;
}
const pod5LinuxPath = toWSLPath(pod5WinPath);
const outputLinuxPath = `${pod5LinuxPath}/${outputBam}`;
const args = [
"dorado basecaller -rv",
` --kit-name ${kitInput.value}`,
` --min-qscore ${qscoreInput.value}`
];
// Add custom barcode flags only if both paths are provided
if (barcodeToml && barcodeFasta) {
args.push(` --barcode-arrangement ${toWSLPath(barcodeToml)}`);
args.push(` --barcode-sequences ${toWSLPath(barcodeFasta)}`);
}
args.push(` ${modelInput.value}`);
args.push(` "${pod5LinuxPath}" > "${outputLinuxPath}"`);
textarea.value = `# 🧬 Run Dorado Basecalling\n${args.join(" \\\n")}`;
copyButton.disabled = false;
}
copyButton.onclick = () => {
navigator.clipboard.writeText(textarea.value);
copyButton.textContent = "✅ Copied!";
setTimeout(() => (copyButton.textContent = "📋 Copy Command"), 1500);
};
[
pod5FolderInput,
outputPathInput,
modelInput,
kitInput,
qscoreInput,
barcodeArrangementInput,
barcodeSequencesInput
].forEach((input) => input.addEventListener("input", updateScript));
updateScript();
const controls = html`<div style="display: flex; flex-direction: column; gap: 1em; min-width: 360px;">
${kitInput}
${modelInput}
${qscoreInput}
${pod5FolderInput}
${outputPathInput}
${barcodeArrangementInput}
${barcodeSequencesInput}
</div>`;
const output = html`<div style="flex-grow: 1; display: flex; flex-direction: column; gap: 0.5em;">
${textarea}
${copyButton}
</div>`;
return html`<div style="display: flex; gap: 2em; align-items: flex-start;">
${controls}
${output}
</div>`;
}
Purpose-built for displays of data
Observable is your go-to platform for exploring data and creating expressive data visualizations. Use reactive JavaScript notebooks for prototyping and a collaborative canvas for visual data exploration and dashboard creation.
