Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget;
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Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget;
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Stars31,545
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LanguagePython
LicenseMIT
📦 Ships with scientific-agent-skills
</> SKILL.md
biopython.SKILL.md
---name: biopython
description: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
allowed-tools: Read Write Edit Bash
compatibility: Requires Python 3.10+, NumPy, and Biopython. Entrez and web BLAST examples require network access; local BLAST/MUSCLE examples require those command-line tools installed separately.
license: Biopython License Agreement
required_environment_variables: [{"name": "NCBI_EMAIL", "prompt": "Email for NCBI Entrez identification (required by NCBI policy for Entrez calls).", "required_for": "optional features"}, {"name": "NCBI_API_KEY", "prompt": "NCBI API key to raise Entrez rate limits.", "required_for": "optional features"}]
metadata: {"version": "1.2", "skill-author": "K-Dense Inc.", "openclaw": {"envVars": [{"name": "NCBI_EMAIL", "required": false, "description": "Email for NCBI Entrez identification (required by NCBI policy for Entrez calls)."}, {"name": "NCBI_API_KEY", "required": false, "description": "NCBI API key to raise Entrez rate limits."}]}}
---# Biopython: Computational Molecular Biology in Python
## Overview
Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. The current version is **Biopython 1.87** (released 30 March 2026). It supports **Python 3.10-3.14** and PyPy3.10, and requires NumPy. Biopython 1.87 also addresses **CVE-2025-68463** in `Bio.Entrez.Parser` when parsing untrusted files, so prefer 1.87+ for workflows that parse externally supplied Entrez XML.
Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains:
1. **Sequence Handling** - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O
2. **Alignment Analysis** - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments
3. **Database Access** - Bio.Entrez for programmatic access to NCBI databases
4. **BLAST Operations** - Bio.Blast for running and parsing BLAST searches
5. **Structural Bioinformatics** - Bio.PDB for working with 3D protein structures
6. **Phylogenetics** - Bio.Phylo for phylogenetic tree manipulation and visualization
7. **Advanced Features** - Motifs, population genetics, sequence utilities, and more
## Installation and Setup
Install the current stable Biopython release with an explicit version pin for reproducibility:
```bash
uv pip install "biopython==1.87"
```
For NCBI database access, always set your email address (required by NCBI). For reusable software, set a stable `Entrez.tool` value and register the tool/email with NCBI. For higher rate limits (10 req/s instead of 3 req/s), read only `NCBI_API_KEY` from the environment — do not hardcode keys or load unrelated environment variables:
```python
import os
from Bio import Entrez
Entrez.email = "your.email@example.com" # required — use your real email
Entrez.tool = "your_tool_name" # optional but recommended for reusable software
# Optional: register at https://www.ncbi.nlm.nih.gov/account/settings/
if api_key := os.environ.get("NCBI_API_KEY"):
Entrez.api_key = api_key
```
## Using This Skill
This skill provides comprehensive documentation organized by functionality area. When working on a task, consult the relevant reference documentation:
### 1. Sequence Handling (Bio.Seq & Bio.SeqIO)
**Reference:** `references/sequence_io.md`
Use for:
- Creating and manipulating biological sequences
- Reading and writing sequence files (FASTA, GenBank, FASTQ, etc.)
- Converting between file formats
- Extracting sequences from large files
- Sequence translation, transcription, and reverse complement
- Working with SeqRecord objects
**Quick example:**
```python
from Bio import SeqIO
# Read sequences from FASTA file
for record in SeqIO.parse("sequences.fasta", "fasta"):
1. **Always read relevant reference documentation** before writing code
2. **Use grep to search reference files** for specific functions or examples
3. **Validate file formats** before parsing
4. **Handle missing data gracefully** - Not all records have all fields
5. **Cache downloaded data** - Don't repeatedly download the same sequences
6. **Respect NCBI rate limits** - Use API keys, registered tool/email values for reusable software, and Entrez history/batching for large jobs
7. **Test with small datasets** before processing large files
8. **Keep Biopython updated** to get latest features and bug fixes
9. **Use appropriate genetic code tables** for translation
10. **Document analysis parameters** for reproducibility
## Troubleshooting Common Issues
### Issue: "No handlers could be found for logger 'Bio.Entrez'"
**Solution:** This is just a warning. Set Entrez.email to suppress it.
### Issue: "HTTP Error 400" from NCBI
**Solution:** Check that IDs/accessions are valid and properly formatted.
### Issue: "ValueError: EOF" when parsing files
**Solution:** Verify file format matches the specified format string.
### Issue: Alignment fails with "sequences are not the same length"
**Solution:** Ensure sequences are aligned before using AlignIO or MultipleSeqAlignment.
### Issue: BLAST searches are slow
**Solution:** Use local BLAST for large-scale searches, or cache results.
### Issue: PDB parser warnings
**Solution:** Use `PDBParser(QUIET=True)` to suppress warnings, or investigate structure quality.
### Issue: ImportError for Bio.HMM, Bio.MarkovModel, or Bio.Application
**Solution:** These modules were removed in Biopython 1.86. Use [hmmlearn](https://pypi.org/project/hmmlearn/) for HMMs and the standard library `subprocess` module instead of `Bio.Application` CLI wrappers.
### Issue: PairwiseAligner returns fewer alignments after upgrading to 1.86+
**Solution:** The default gap score changed from 0 to -1 in 1.86, eliminating trivial tie alignments. Set `aligner.gap_score = 0` to restore the old behavior if needed (see `references/alignment.md`).
