alterlab-biopython

Files (9)

• SKILL.md
• evals.json · evals/
• advanced.md · references/
• alignment.md · references/
• blast.md · references/
• databases.md · references/
• phylogenetics.md · references/
• sequence_io.md · references/
• structure.md · references/

SKILL.md (first lines)

# 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 1.88** (August 2026), which supports Python 3.10–3.14 and requires NumPy.

> **Removed / changed APIs to watch for**
>
> - **Command-line wrappers are gone.** `Bio.Application` and everything built on it —
>   `Bio.Blast.Applications` (`Ncbiblastn/p/x…Commandline`, `NcbimakeblastdbCommandline`) and
>   `Bio.Align.Applications` (`ClustalOmegaCommandline`, `MuscleCommandline`) — were
>   deprecated in 1.78 and **removed in 1.86**. Call the executables through `subprocess`
>   (see `references/blast.md` and `references/alignment.md`).
> - **PairwiseAligner gap scores changed in 1.86.** The default gap score is now **-1**
>   (was 0), so an aligner left at defaults returns far fewer, non-degenerate alignments.
>   The gap attributes were also renamed to insertion/deletion forms
>   (`open_internal_insertion_score`, …); the `*_gap_score` names still work as
>   meta-attributes. The `alphabet` attribute is deprecated and unused.
> - **`Bio.pairwise2` is deprecated** — use `Bio.Align.PairwiseAligner`.
> - **`Bio.Blast.NCBIXML` is declared obsolete** as of the 1.89 development line in favour
>   of the `Bio.Blast` parser added in 1.84 (`Blast.parse`/`Blast.read`, `Blast.qblast`).
>   It still ships and works in 1.88; prefer the new API for new code.
> - **Security fixes worth upgrading for:** 1.87 fixed CVE-2025-68463 in
>   `Bio.Entrez.Parser`, and 1.88 removed an `eval` in the `Bio.Nexus` parser that allowed
>   code execution from a malicious NEXUS file. Treat downloaded records as untrusted input
>   and keep Biopython current.

## When to Use This Skill

Use this skill when:

- Working with biological sequences (DNA, RNA, or protein)
- Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)
- Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez
- Running BLAST searches or parsing BLAST results
- Performing sequence alignments (pairwise or multiple sequence alignments)
- Analyzing protein structures from PDB files
- Creating, manipulating, or visualizing phylogenetic trees
- Finding sequence motifs or analyzing motif patterns
- Calculating sequence statistics (GC content, molecular weight, melting temperature, etc.)
- Performing structural bioinformatics tasks
- Working with population genetics data
- Any other computational molecular biology task

### Does NOT Trigger

| Scenario | Use Instead |
|----------|-------------|
| Running local BLAST+ / `makeblastdb` from the command line, or DIAMOND | `alterlab-blast` |
| A one-line lookup of a gene, sequence, or structure | `alterlab-gget` |
| One call across many web services (UniProt + KEGG + ChEMBL in a pipeline) | `alterlab-bioservices` |
| SAM/BAM/CRAM record access, pileups, and read filtering | `alterlab-pysam` |
| Building an ML phylogeny from unaligned sequences (MAFFT + IQ-TREE) | `alterlab-phylogenetics` |

## Core Capabilities

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 Biopython (requires Python 3 and NumPy). On this machine, prefer running scripts with `uv run`:

```bash
# Ad-hoc: run a script with Biopython available, no venv to manage
uv run --with biopython script.py

# Or add it to a project
uv add biopython
```

For NCBI database access, always set your email address (required by NCBI):

```python
from Bio import Entrez
Entrez.email = "your.email@example.com"

# Optional: API key for higher rate limits (10 req/s instead of 3 req/s)
Entrez.api_key = "your_api_key_here"
```

## 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"):
    print(f"{record.id}: {len(record.seq)} bp")

# Convert GenBank to FASTA
SeqIO.convert("input.gb", "genbank", "output.fasta", "fasta")
```

### 2. Alignment Analysis (Bio.Align & Bio.AlignIO)

**Reference:** `references/alignment.md`

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