// src/utils/formatting.ts
import { VariantResult, RegionResult, BatchResult } from '../types.js';
/**
* Format variant prediction result as beautiful Markdown
*/
export function formatVariantResult(result: VariantResult): string {
const date = new Date().toISOString().split('T')[0];
const time = new Date().toISOString().split('T')[1].split('.')[0];
let output = `# 🧬 AlphaGenome Variant Analysis\n\n`;
output += `**Variant**: ${result.variant}\n`;
if (result.gene_context) {
output += `**Gene Context**: ${result.gene_context}\n`;
}
output += `**Analysis Date**: ${date} ${time} UTC\n\n`;
output += `---\n\n`;
// Summary table
output += `## 📊 Regulatory Impact Summary\n\n`;
output += `| Metric | Reference | Alternate | Change | Impact Level |\n`;
output += `|--------|-----------|-----------|--------|--------------||\n`;
if (result.predictions.rna_seq) {
const rna = result.predictions.rna_seq;
const change = (
((rna.alternate_score - rna.reference_score) / rna.reference_score) *
100
).toFixed(0);
const arrow = parseFloat(change) < 0 ? '↓' : '↑';
const level =
Math.abs(parseFloat(change)) > 50
? '🔴 High'
: Math.abs(parseFloat(change)) > 20
? '🟡 Moderate'
: '🟢 Low';
output += `| RNA Expression | ${rna.reference_score.toFixed(
2
)} | ${rna.alternate_score.toFixed(2)} | ${change}% ${arrow} | ${level} |\n`;
}
if (result.predictions.splice) {
const splice = result.predictions.splice;
const change = (splice.delta * 100).toFixed(0);
const arrow = splice.delta < 0 ? '↓' : '↑';
const level = Math.abs(splice.delta) > 0.2 ? '🟡 Moderate' : '🟢 Low';
output += `| Splice Score | ${splice.reference_score.toFixed(
2
)} | ${splice.alternate_score.toFixed(2)} | ${change}% ${arrow} | ${level} |\n`;
}
output += `\n**Overall Impact**: ${getImpactBadge(result.interpretation.impact_level)}\n\n`;
output += `---\n\n`;
// Detailed analysis
output += `## 🔬 Detailed Analysis\n\n`;
if (result.predictions.rna_seq) {
const rna = result.predictions.rna_seq;
output += `### RNA Expression Impact\n`;
output += `- **Prediction Confidence**: ${rna.confidence.toFixed(2)} (${getConfidenceLabel(
rna.confidence
)})\n`;
output += `- **Fold Change**: ${rna.fold_change.toFixed(2)}x ${
rna.fold_change < 0 ? 'decrease' : 'increase'
}\n`;
output += `- **Mechanism**: Likely affects ${
rna.fold_change < 0 ? 'promoter activity' : 'enhancer activation'
}\n\n`;
}
if (result.predictions.splice) {
const splice = result.predictions.splice;
output += `### Splicing Analysis\n`;
output += `- **Consequence**: ${splice.consequence.replace(/_/g, ' ')}\n`;
output += `- **Clinical Relevance**: ${getSpliceRelevance(splice.delta)}\n\n`;
}
if (result.predictions.tf_binding && result.predictions.tf_binding.length > 0) {
output += `### Transcription Factor Binding\n`;
output += `**Disrupted Sites** (${result.predictions.tf_binding.length} found):\n`;
result.predictions.tf_binding.forEach((tf, i) => {
const pct = (tf.change * 100).toFixed(0);
output += `${i + 1}. **${tf.factor}** binding site\n`;
output += ` - Reference score: ${tf.ref_score.toFixed(2)}\n`;
output += ` - Alternate score: ${tf.alt_score.toFixed(2)}\n`;
output += ` - Change: ${pct}% ${tf.change < 0 ? '↓' : '↑'}\n\n`;
});
}
// Clinical interpretation
output += `---\n\n`;
output += `## 🎯 Clinical Interpretation\n\n`;
output += `### Impact Classification\n`;
output += `**${result.interpretation.clinical_significance?.toUpperCase() || 'UNCERTAIN'}** `;
output += `(${result.interpretation.impact_level} confidence)\n\n`;
if (result.interpretation.recommendations.length > 0) {
output += `### Recommendations\n`;
result.interpretation.recommendations.forEach((rec) => {
output += `- 🔬 ${rec}\n`;
});
output += `\n`;
}
// Disclaimer
output += `---\n\n`;
output += `## ⚠️ Important Disclaimer\n\n`;
output += `**For Research Use Only**\n\n`;
output += `- ⚠️ NOT for clinical diagnosis or treatment decisions\n`;
output += `- ✅ Powered by Google DeepMind's AlphaGenome AI\n`;
output += `- ✅ Predictions based on multi-modal genomic data\n`;
output += `- 📋 Always validate findings with wet-lab experiments\n\n`;
output += `---\n\n`;
output += `*AlphaGenome MCP Server v0.1.0*\n`;
output += `*GitHub: https://github.com/taehojo/alphagenome-mcp*\n`;
return output;
}
/**
* Format region analysis result as beautiful Markdown
*/
export function formatRegionResult(result: RegionResult): string {
const date = new Date().toISOString().split('T')[0];
const time = new Date().toISOString().split('T')[1].split('.')[0];
let output = `# 🔍 AlphaGenome Region Analysis\n\n`;
output += `**Region**: ${result.region}\n`;
output += `**Analysis Date**: ${date} ${time} UTC\n\n`;
output += `---\n\n`;
output += `## 📊 Regulatory Elements Detected\n\n`;
if (result.elements.promoters && result.elements.promoters.length > 0) {
output += `### Promoters (${result.elements.promoters.length} found)\n`;
result.elements.promoters.forEach((p, i) => {
output += `${i + 1}. **Position**: ${p.start.toLocaleString()}-${p.end.toLocaleString()}\n`;
output += ` - **Score**: ${p.score.toFixed(2)} (${getConfidenceLabel(p.score)})\n`;
output += ` - **Type**: ${p.type.replace(/_/g, ' ')}\n`;
if (p.associated_gene) {
output += ` - **Associated Gene**: ${p.associated_gene}\n`;
}
if (p.activity) {
output += ` - **Activity**: ${p.activity}\n`;
}
output += `\n`;
});
}
if (result.elements.enhancers && result.elements.enhancers.length > 0) {
output += `### Enhancers (${result.elements.enhancers.length} found)\n`;
result.elements.enhancers.forEach((e, i) => {
output += `${i + 1}. **Position**: ${e.start.toLocaleString()}-${e.end.toLocaleString()}\n`;
output += ` - **Score**: ${e.score.toFixed(2)} (${getConfidenceLabel(e.score)})\n`;
if (e.type) {
output += ` - **Type**: ${e.type.replace(/_/g, ' ')}\n`;
}
if (e.target_gene) {
output += ` - **Target Gene**: ${e.target_gene}\n`;
}
if (e.distance_to_tss) {
output += ` - **Distance to TSS**: ${e.distance_to_tss.toLocaleString()} bp\n`;
}
if (e.chromatin_loop) {
output += ` - **Chromatin Loop**: Confirmed by Hi-C\n`;
}
output += `\n`;
});
}
if (result.elements.tf_binding_sites && result.elements.tf_binding_sites.length > 0) {
output += `### Transcription Factor Binding Sites (${result.elements.tf_binding_sites.length} found)\n\n`;
output += `**High-confidence sites** (score > 0.8):\n`;
const highConf = result.elements.tf_binding_sites.filter((s) => s.score > 0.8);
highConf.forEach((s) => {
output += `- **${s.factor}** (${s.position.toLocaleString()}): Score ${s.score.toFixed(
2
)} [${s.strand}]\n`;
});
output += `\n`;
}
if (result.elements.chromatin_states && result.elements.chromatin_states.length > 0) {
output += `### Chromatin State Map\n\n`;
output += `| Position Range | State | Activity |\n`;
output += `|----------------|-------|----------|\n`;
result.elements.chromatin_states.forEach((cs) => {
output += `| ${cs.start.toLocaleString()}-${cs.end.toLocaleString()} | ${
cs.state
} | ${cs.activity} |\n`;
});
output += `\n`;
}
output += `---\n\n`;
output += `## ⚠️ Important Disclaimer\n\n`;
output += `**For Research Use Only**\n\n`;
output += `- ⚠️ NOT for clinical use or diagnosis\n`;
output += `- ✅ Powered by AlphaGenome AI predictions\n`;
output += `- 📋 Validate with experimental data\n\n`;
output += `---\n\n`;
output += `*AlphaGenome MCP Server v0.1.0*\n`;
output += `*GitHub: https://github.com/taehojo/alphagenome-mcp*\n`;
return output;
}
/**
* Format batch scoring result as beautiful Markdown
*/
export function formatBatchResult(result: BatchResult): string {
const date = new Date().toISOString().split('T')[0];
const time = new Date().toISOString().split('T')[1].split('.')[0];
let output = `# 📊 AlphaGenome Batch Variant Analysis\n\n`;
output += `**Total Variants Analyzed**: ${result.total_analyzed}\n`;
output += `**Analysis Date**: ${date} ${time} UTC\n\n`;
output += `---\n\n`;
output += `## 🏆 Top Variants by Impact\n\n`;
output += `| Rank | Variant ID | Location | Impact Score | Impact Level | Key Effect |\n`;
output += `|------|------------|----------|--------------|--------------|------------|\n`;
result.variants.forEach((v) => {
const badge =
v.impact_level === 'high'
? '🔴 High'
: v.impact_level === 'moderate'
? '🟡 Moderate'
: '🟢 Low';
const varId = v.variant_id || '-';
const keyEffect = v.key_effect || 'Regulatory element';
output += `| ${v.rank} | ${varId} | ${v.variant} | ${v.score.toFixed(
2
)} | ${badge} | ${keyEffect} |\n`;
});
output += `\n---\n\n`;
output += `## 📈 Impact Distribution\n\n`;
output += `\`\`\`\n`;
output += `Impact Level | Count | Percentage\n`;
output += `----------------|-------|------------\n`;
for (const [level, count] of Object.entries(result.distribution)) {
const pct = ((count / result.total_analyzed) * 100).toFixed(1);
const emoji = level === 'high' ? '🔴' : level === 'moderate' ? '🟡' : '🟢';
output += `${emoji} ${level.padEnd(13)} | ${String(count).padStart(5)} | ${pct.padStart(5)}%\n`;
}
output += `----------------|-------|------------\n`;
output += `Total | ${String(result.total_analyzed).padStart(5)} | 100.0%\n`;
output += `\`\`\`\n\n`;
output += `---\n\n`;
output += `## ⚠️ Important Disclaimer\n\n`;
output += `**For Research Use Only**\n\n`;
output += `- ⚠️ NOT for clinical use or diagnosis\n`;
output += `- ✅ Powered by AlphaGenome AI predictions\n`;
output += `- 📋 Validate with experimental data\n\n`;
output += `---\n\n`;
output += `*AlphaGenome MCP Server v0.1.0*\n`;
output += `*GitHub: https://github.com/taehojo/alphagenome-mcp*\n`;
return output;
}
// ============================================================================
// Helper Functions
// ============================================================================
function getImpactBadge(level: string): string {
switch (level) {
case 'critical':
case 'high':
return '🔴 HIGH RISK ⚠️';
case 'moderate':
return '🟡 MODERATE RISK';
case 'low':
return '🟢 LOW RISK';
default:
return '⚪ UNKNOWN';
}
}
function getConfidenceLabel(score: number): string {
if (score >= 0.9) return 'Very High';
if (score >= 0.7) return 'High';
if (score >= 0.5) return 'Moderate';
return 'Low';
}
function getSpliceRelevance(delta: number): string {
const abs = Math.abs(delta);
if (abs > 0.3) return 'High - May cause aberrant splicing';
if (abs > 0.15) return 'Moderate - Could affect splicing';
return 'Low - Minimal splicing impact';
}
