biopython
Pass
Audited by Gen Agent Trust Hub on Feb 20, 2026
Risk Level: SAFECOMMAND_EXECUTIONPROMPT_INJECTION
Full Analysis
- COMMAND_EXECUTION (SAFE): The file 'references/alignment.md' demonstrates the use of 'ClustalOmegaCommandline' and 'MuscleCommandline'. These are standard Biopython wrappers used to interface with external alignment binaries. While this involves subprocess execution, it is the primary intended functionality of the library for bioinformatics workflows.
- PROMPT_INJECTION (SAFE): The skill provides instructions for parsing external data formats like FASTA and GenBank using 'Bio.SeqIO' and 'Bio.AlignIO', which constitutes an indirect prompt injection surface. Evidence: 1. Ingestion points: 'SeqIO.parse' and 'AlignIO.read' in 'references/sequence_io.md' and 'references/alignment.md'. 2. Boundary markers: Absent. 3. Capability inventory: Potential command execution through alignment tools and file system operations. 4. Sanitization: No sanitization or validation of sequence metadata is shown in the reference snippets.
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