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Filter Sequences - Usage Guide

Overview

This skill enables AI agents to help you filter and select sequences based on various criteria using Biopython.

Prerequisites

pip install biopython

Quick Start

Tell your AI agent what you want to do:

  • "Keep only sequences longer than 500 bp"
  • "Extract sequences matching these IDs"
  • "Filter out sequences with N's"
  • "Select sequences with GC content between 40-60%"

Example Prompts

By Length

"Remove sequences shorter than 200 bp from my FASTA file"

By ID

"Extract sequences with IDs listed in wanted_ids.txt"

By Content

"Filter out sequences containing more than 5% N bases"

By GC Content

"Keep only sequences with GC content above 50%"

Combined

"Filter sequences: length >= 100, no N's, GC 40-60%"

What the Agent Will Do

  1. Load sequences from input file
  2. Apply specified filter criteria
  3. Keep sequences passing all filters
  4. Write filtered sequences to output

Tips

  • Use generator expressions for large files (memory efficient)
  • For ID-based filtering, use sets for O(1) lookup
  • Combine multiple criteria in a single filter function
  • Generators can only be used once - recreate if needed