Build a Gene Data Package FASTA Cleanser and Telemetry Monitor

Process multi-FASTA gene packages to detect non-IUPAC nucleotide characters and low-complexity repeats. Track data cleansing performance and error drift using Langfuse.

Bioinformatics Pipeline Engineer

Stream multi-FASTA files from NCBI Datasets gene archives using Biopython SeqIO.

Scan each sequence entry for non-IUPAC nucleotide symbols, masked N-stretches, and degenerate codons.

Log cleaning latency, token counts, and sequence anomaly rates into Langfuse telemetry spans.

Export sanitized FASTA output alongside a structured data cleaning audit log.

Command-line pipeline configured with environment variables sending real-time telemetry to Langfuse UI.

Generate synthetic multi-FASTA files containing random mutations, non-IUPAC characters, and poly-N stretches. Starter examples below are synthetic. They are not downloaded records.

Biopython Employs Biopython's Bio.SeqIO and sequence validation routines to inspect sequence headers and character contents.

langfuse, biopython, pydantic. Langfuse provides observability, trace tracking, and latency metrics for repetitive data curation pipelines. Local or hosted LLM for generating contextual summaries of sequence anomaly clusters.

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.

Correctly identifies non-standard IUPAC characters (e.g. 'Z', '?', numbers) in input FASTA records.

Sends telemetry traces to Langfuse containing sequence identifier and processing duration.

Generates sanitized FASTA files preserving sequence IDs and valid biological characters.

```json [ { "input": { "record_id": "TRANS_001", "raw_sequence": "ATGCGTACNNNGTACG" }, "expected_output": { "valid_iupac": true, "n_ratio": 0.1875, "sanitized_sequence": "ATGCGTACNNNGTACG", "telemetry_logged": true } }, { "input": { "record_id": "TRANS_002", "raw_sequence": "ATGC123GZZTAG" }, "expected_output": { "valid_iupac": false, "invalid_characters": [ "1", "2", "3", "Z" ], "sanitized_sequence": "ATGCGGTAG", "telemetry_logged": true } } ] ```

Processes pure nucleotide strings from public or synthetic data without clinical patient associations. Use mock external writes. Require human review before any real deployment.