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Define Pydantic AI Bacterial Screener Agent

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Linked challenge: Bacterial PCR Leaping Artifact Filter and Gene Screener with Pydantic AI

Format
Code-aware
Lines
12
Sections
3
Linked challenge
Bacterial PCR Leaping Artifact Filter and Gene Screener with Pydantic AI

Prompt source

Original prompt text with formatting preserved for inspection.

12 lines
3 sections
No variables
0 checklist items
from pydantic import BaseModel, Field
from pydantic_ai import Agent

class ReadAnalysisResult(BaseModel):
    read_id: str
    is_pcr_leaping_artifact: bool = Field(description='True if chimeric PCR jump detected')
    target_amr_gene: str | None = Field(default=None, description='Detected antimicrobial resistance gene')

# Initialize Pydantic AI agent with structured result type
bacterial_agent = Agent(
    'openai:gpt-4o',
    result_type=ReadAnalysisResult,
    system_prompt='Analyze bacterial sequence reads and flag PCR leaping artifacts vs AMR gene markers.'
)

Adaptation plan

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Keep stable

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Tune next

Update libraries, interfaces, and environment assumptions to match the stack you actually run.

Verify after

Test failure handling, edge cases, and any code paths that depend on hidden context or secrets.