biopython
Pass
Audited by Gen Agent Trust Hub on Feb 17, 2026
Risk Level: SAFECOMMAND_EXECUTIONPROMPT_INJECTION
Full Analysis
- COMMAND_EXECUTION (LOW): The file
references/alignment.mddocuments the use ofClustalOmegaCommandlineandMuscleCommandline. These are Biopython wrappers that execute external alignment binaries on the host system. While these are intended features for bioinformatics, they represent a potential surface for command execution if inputs are not properly sanitized.\n- PROMPT_INJECTION (LOW): The documented patterns for reading external sequence files combined with command execution capabilities create a surface for indirect prompt injection (Category 8) if the agent processes untrusted bio-data files.\n - Ingestion points:
references/sequence_io.mdandreferences/alignment.md(SeqIO.parse,AlignIO.read,AlignIO.parse).\n - Boundary markers: Absent in documentation examples.\n
- Capability inventory: Execution of external binaries via
Bio.Align.Applicationswrappers.\n - Sanitization: No input validation or sanitization is demonstrated in the provided code snippets.
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