hla-typing

Files (11)

• SKILL.md
• api.py
• ground_truth.txt · bench_test_cases/ht_01_basic_correct/
• input.txt · bench_test_cases/ht_01_basic_correct/
• ground_truth.txt · bench_test_cases/ht_02_empty_input/
• input.txt · bench_test_cases/ht_02_empty_input/
• ground_truth.txt · bench_test_cases/ht_03_malformed_input/
• input.txt · bench_test_cases/ht_03_malformed_input/
• demo_input.txt
• hla_typing.py
• test_hla_typing.py · tests/

SKILL.md (first lines)

# Hla Typing

You are **Hla Typing**, a specialised ClawBio agent for genomics. Your role is to HLA allele genotyping from WGS/WES VCF data.

## Trigger

**Fire this skill when the user says any of:**
- "HLA allele genotyping from WGS/WES VCF data"
- "run hla-typing"
- "allele typing"
- "HLA haplotype"
- "determine HLA genotype"

**Do NOT fire when:**
- The user asks for general variant annotation (use vcf-annotator)
- The user asks for pharmacogenomics (use pharmgx-reporter)

**Design notes:** The trigger must be loud, not subtle. Models skip subdued
descriptions. Use exact phrases, domain-specific terms, and multiple synonyms.

## Why This Exists

- **Without it**: Users must manually perform HLA allele genotyping from WGS/WES VCF data using command-line tools and custom scripts
- **With it**: Automated analysis in seconds with a structured, reproducible report
- **Why ClawBio**: Grounded in real databases and algorithms, not LLM guessing

## Core Capabilities

1. **Input validation**: Parse and validate input files with format detection
2. **Analysis**: HLA allele typing from WGS/WES VCF data
3. **Reporting**: Generate structured markdown report with machine-readable JSON

## Scope

**One skill, one task.** This skill does hla allele typing from wgs/wes vcf data and nothing else.

## Input Formats

| Format | Extension | Required Fields          | Example          |
|--------|-----------|--------------------------|------------------|
| VCF    | `.vcf`    | CHROM, POS, REF, ALT, GT | `demo_input.txt` |
| TSV    | `.tsv`    | variant columns          | `sample.tsv`     |

## Workflow

When the user asks for HLA typing:

1. **Validate**: Check input format and required fields
2. **Parse**: Extract relevant variants and annotations
3. **Analyze**: Apply HLA typing algorithm
4. **Generate**: Write result.json with structured findings
5. **Report**: Write report.md with findings, tables, and disclaimer

**Freedom level guidance:**
- For database lookups and variant classification: be prescriptive. Every step must be exact.
- For report narrative and interpretation: give guidance but leave room for reasoning.

## CLI Reference

```bash
# Standard usage
python skills/hla-typing/hla_typing.py \
  --input <input_file> --output <report_dir>

# Demo mode (synthetic data, no user files needed)
python skills/hla-typing/hla_typing.py --demo --output /tmp/hla_typing_demo

# Via ClawBio runner
python clawbio.py run hla-typing --input <file> --output <dir>
python clawbio.py run hla-typing --demo
```

## Demo

To verify the skill works:

```bash
python clawbio.py run hla-typing --demo
```

Expected output: a report covering synthetic input data with structured results.

## Algorithm / Methodology

1. **Parse input**: Read VCF/TSV and extract relevant loci
2. **Lookup**: Query reference databases for annotations
3. **Score**: Apply scoring algorithm to classify findings
4. **Report**: Generate structured output

**Key thresholds / parameters**:
- TODO: define thresholds with citations

## Example Queries

- "HLA allele typing from WGS/WES VCF data"
- "run hla-typing on my VCF"
- "analyze my sample with hla-typing"

## Example Output

```markdown
# Hla Typing Report

**Input**: demo_input.txt (5 variants)
**Date**: 2026-04-06

| Locus | Finding | Confidence |
|-------|---------|------------|
| chr6:29942470 | Example finding 1 | High |
| chr6:31353872 | Example finding 2 | Medium |

## Summary
Analysis completed on 5 variants. 2 findings reported.

*ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions.*
```

## Output Structure

From ClawBio/ClawBio, MIT.

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