Define Pydantic AI Bacterial Screener Agent

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

Prompt source

implementation12 lines3 sectionsNo variables0 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.'
)