Build a Protein Accession Translation Conformance Auditor — implementation

## Build
Cross-reference NCBI protein fasta records against CDS translation products using Biopython. Convert validated peptide sequences and mismatch scores into FHIR Molecular Observation entries.

## User
Genomic Translation Specialist

## Workflow
1. Ingest CDS and protein FASTA sequences from an NCBI Datasets gene archive.
2. Translate nucleotide coding sequences into amino acid strings using standard Biopython codon tables.
3. Compute sequence alignment identity between translated CDS and RefSeq protein records.
4. Format verified identity percentages into FHIR Molecular Observation bundles for export.

## Interface
Terminal CLI and static web viewer showing sequence identity scores, translation offsets, and validation status.

## Data
Use synthetic FASTA pairs derived from NCBI Datasets human TP53 test packages stored in a mock test directory.
Starter examples below are synthetic. They are not downloaded records.

## Source
[Biopython](https://raw.githubusercontent.com/biopython/biopython/master/README.rst)
Uses Biopython computational molecular biology routines to perform nucleotide translation and pairwise sequence comparisons.

## Tools
ollama, biopython, click.
ollama runs lightweight local open-source LLMs to classify biological mutation notes into FHIR observation annotations.
Local Ollama instance serving a 7B-8B parameter model alongside local Python 3.12 environment.

## Deliverables
Submit runnable source, pinned dependencies, setup commands, a working interface, example outputs, and a recorded end-to-end demo. Include tests and an action log.

## Acceptance
- Biopython translation accurately reproduces protein sequence for standard transcripts.
- Generate FHIR Observation with component identity percentage matching computed alignment score.
- Route sequences exhibiting less than 99% peptide identity to manual review.

## Starter Examples
```json
[
  {
    "input": {
      "cds_id": "NM_000546.6_cds",
      "protein_id": "NP_000537.3",
      "cds_sequence": "ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCGCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACTAAGCGAGCACTGCCCAACAACACCAGCTCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCCTTCAGATCCGTGGGCGTGAGCGCTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGGAAGGAGCCAGGGGGGAGCAGGGCTCACTCCAGCCACCTGAAGTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTCATGTTCAAGACAGAAGGGCCTGACTCAGACTGA",
      "protein_sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD"
    },
    "expected_output": {
      "cds_id": "NM_000546.6_cds",
      "protein_id": "NP_000537.3",
      "translation_match": true,
      "identity_percent": 100,
      "fhir_observation": {
        "resourceType": "Observation",
        "status": "final",
        "valueQuantity": {
          "value": 100,
          "unit": "%"
        }
      }
    }
  },
  {
    "input": {
      "cds_id": "NM_000546.6_cds_err",
      "protein_id": "NP_000537.3",
      "cds_sequence": "ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCA",
      "protein_sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP"
    },
    "expected_output": {
      "cds_id": "NM_000546.6_cds_err",
      "protein_id": "NP_000537.3",
      "translation_match": false,
      "identity_percent": 33.33,
      "fhir_observation": {
        "resourceType": "Observation",
        "status": "preliminary",
        "valueQuantity": {
          "value": 33.33,
          "unit": "%"
        }
      }
    }
  }
]
```

## Safety
Strictly research compute evaluating nucleotide-to-peptide translation consistency. No diagnostic interpretation or medical recommendation.
Use mock external writes. Require human review before any real deployment.