wes-clinical-report-es

Informe Clinico WES en Espanol

Skill for generating professional clinical PDF reports in Spanish from whole exome sequencing (WES) data. Designed for Novogene WES data (GATK + ANNOVAR pipeline) but adaptable to any WES pipeline with equivalent annotations. Translates all section headings, table headers, cell values, and interpretive text from English markdown input to Spanish PDF output.

Trigger

Fire this skill when the user says any of:

• "informe clinico WES"
• "generar informe exoma en espanol"
• "clinical report in Spanish"
• "Novogene report Spanish"
• "exome PDF report Spanish"
• "Predice/Inbiomedic report"

Do NOT fire when:

• User asks for an English report (use wes-clinical-report-en)
• User asks for variant annotation only (use variant-annotation)
• User asks for ACMG classification only (use clinical-variant-reporter)

Scope

One skill, one task: convert WES markdown reports (English input) into professional Spanish-language clinical PDFs with full translation and clinical interpretation.

Workflow

1. Parse WES markdown report (structured sections 1-7)
2. Extract KPI metrics from Exome Summary
3. Extract pathogenic variants, PGx alerts, rare damaging variants
4. Translate all headings, table headers, cell values, and body text to Spanish
5. Build interpretive summary paragraph in Spanish
6. Render all sections as styled PDF with clinical tables
7. Add ancestry estimation (section 8) if data available
8. Add limitations section (section 9) in Spanish
9. Add Spanish disclaimer and report metadata
10. Output PDF to specified directory

Capabilities

1. Clinical interpretation summary (Spanish): key findings, high-risk PGx alerts, prioritised rare variants, clinical follow-up recommendations.
2. Full translation layer: section headings, table headers, metric labels, zygosity, classification, consequence, clinical effects, traits, and interpretations all translated via lookup dictionaries.
3. Clinically significant variants: ClinVar P/LP, ACMG SF v3.2, cancer predisposition panel, conflicting variants.
4. Pharmacogenomics: CPIC star alleles, clinical effects, affected medications with contextualised high-risk alerts.
5. Fitness and nutrition traits: genotypes with evidence grades (Corpas et al. 2021).
6. Rare damaging variant prioritisation: REVEL, CADD, gnomAD AF.
7. Institutional logos: Predice (left) and Inbiomedic (right) on cover and header.

Example Output

Pagina 1 (portada):
  [Logo Predice]                    [Logo Inbiomedic]
  +---------------------------------------------+
  |  Secuenciacion del Exoma Completo  [SampleN]|
  |  Plataforma / Referencia / Fecha            |
  +---------------------------------------------+
  [KPIs: SNPs Totales | Missense | Stopgain | Raras Patog. | ClinVar P/PP]

  Interpretacion de resultados
  (parrafo interpretativo clinico auto-generado en espanol)

Paginas 2+:
  1. Resumen del Exoma
  2. Variantes de Significancia Clinica
  3. Farmacogenomica
  4. Rasgos de Aptitud Fisica y Nutricion
  5. Variantes Raras Patogenicas Priorizadas
  6. Contexto de Enfermedad y Vias Metabolicas
  7. Metodologia
  8. Estimacion de Ancestria
  9. Limitaciones
  [Aviso legal / Disclaimer]

Usage

# Generate reports for all samples
python skills/wes-clinical-report-es/wes_clinical_report_es.py \
  --report-dir /path/to/REPORTS/ \
  --output-dir /path/to/PDF-ES/ \
  --logo-left /path/to/logo_predice.jpg \
  --logo-right /path/to/logo_inbiomedic.jpg

# Generate report for a single sample
python skills/wes-clinical-report-es/wes_clinical_report_es.py \
  --report-dir /path/to/REPORTS/ \
  --output-dir /path/to/PDF-ES/ \
  --samples Sample3

# Demo with default Novogene data
python skills/wes-clinical-report-es/wes_clinical_report_es.py --demo

Input format

The skill consumes WES reports in markdown format generated by the analysis pipeline (scripts 02-12 in ANALYSIS/SCRIPTS/). Each markdown report must follow this structure:

# Whole Exome Sequencing Report: SampleN
> **Project** ... | **Platform** ... | ...
## 1. Exome Summary
## 2. Clinically Significant Variants
## 3. Pharmacogenomics
## 4. Fitness and Nutrition Traits
## 5. Prioritised Rare Damaging Variants
## 6. Disease and Pathway Context
## 7. Methods

Gotchas

1. Input is English, output is Spanish: the markdown reports are in English. The skill translates to Spanish via dictionary lookups. If a term is missing from the translation dictionaries, it appears in English in the PDF. Check untranslated terms in output.
2. Logo paths must exist: if Predice/Inbiomedic logo files are missing, the report still generates but without institutional branding. The script silently skips missing logos.
3. Table truncation: tables with more than 20 rows are truncated in the PDF with a Spanish note to consult TSV files. Do not assume all data is visible in the PDF.
4. ClinVar classifications are time-sensitive: the report reflects ClinVar state at annotation time. Classifications are not permanent.
5. PGx star alleles from SNVs only: CYP2D6 CNV analysis is not included. Do not claim complete metaboliser phenotyping.
6. Hardcoded project ID: the footer references project X202SC26016276-Z01-F001. Update for other projects.

Safety

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.

The Spanish disclaimer in the PDF reads: "Este informe se genera exclusivamente con fines de investigacion y educacion. No es un informe de diagnostico clinico."

Agent Boundary

The agent dispatches and explains; the skill executes. The agent should not modify PDF generation logic inline. All report customisation goes through CLI flags.

Chaining Partners

• variant-annotation: upstream VCF annotation feeding markdown reports
• clinical-variant-reporter: ACMG classification for deeper analysis
• wes-clinical-report-en: English language version of the same report

Maintenance

• Review cadence: quarterly (aligned with ClinVar release cycle)
• Staleness signals: ClinVar version drift, CPIC guideline updates, new Spanish medical terminology standards
• Deprecation: if WES is superseded by WGS-only clinical pipelines

Requirements

• Python 3.9+
• reportlab >= 4.0
• WES markdown reports (see input format above)
• Institutional logos in JPG/PNG (optional)

Privacy

This skill is private and not included in the ClawBio public catalog. It contains institutional logos and clinical report templates that should not be distributed publicly.

References

• Corpas et al. (2021) "Whole Genome Interpretation for a Family of Five" Frontiers in Genetics 12:535123
• CPIC guidelines for pharmacogenomics
• ClinVar / gnomAD / OMIM / COSMIC / KEGG for variant annotation