Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
npxskills add davila7/claude-code-templates--skill biopythonLoading…
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 1.85 (released January 2025), which supports Python 3 and requires NumPy.
Use this skill when:
Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains:
Install Biopython using pip (requires Python 3 and NumPy):
uv pip install biopython
For NCBI database access, always set your email address (required by NCBI):
from Bio import Entrez
Entrez.email = "[email protected]"
# Optional: API key for higher rate limits (10 req/s instead of 3 req/s)
Entrez.api_key = "your_api_key_here"
This skill provides comprehensive documentation organized by functionality area. When working on a task, consult the relevant reference documentation:
Reference: references/sequence_io.md
Use for:
Quick example:
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")
Reference: references/alignment.md
Use for:
Quick example:
from Bio import Align
# Pairwise alignment
aligner = Align.PairwiseAligner()
aligner.mode = 'global'
alignments = aligner.align("ACCGGT", "ACGGT")
print(alignments[0])
Reference: references/databases.md
Use for:
Quick example:
from Bio import Entrez
Entrez.email = "[email protected]"
# Search PubMed
handle = Entrez.esearch(db="pubmed", term="biopython", retmax=10)
results = Entrez.read(handle)
handle.close()
print(f"Found {results['Count']} results")
Reference: references/blast.md
Use for:
Quick example:
from Bio.Blast import NCBIWWW, NCBIXML
# Run BLAST search
result_handle = NCBIWWW.qblast("blastn", "nt", "ATCGATCGATCG")
blast_record = NCBIXML.read(result_handle)
# Display top hits
for alignment in blast_record.alignments[:5]:
print(f"{alignment.title}: E-value={alignment.hsps[0].expect}")
Reference: references/structure.md
Use for:
Quick example:
from Bio.PDB import PDBParser
# Parse structure
parser = PDBParser(QUIET=True)
structure = parser.get_structure("1crn", "1crn.pdb")
# Calculate distance between alpha carbons
chain = structure[0]["A"]
distance = chain[10]["CA"] - chain[20]["CA"]
print(f"Distance: {distance:.2f} Å")
Reference: references/phylogenetics.md
Use for:
Quick example:
from Bio import Phylo
# Read and visualize tree
tree = Phylo.read("tree.nwk", "newick")
Phylo.draw_ascii(tree)
# Calculate distance
distance = tree.distance("Species_A", "Species_B")
print(f"Distance: {distance:.3f}")
Reference: references/advanced.md
Use for:
Quick example:
from Bio.SeqUtils import gc_fraction, molecular_weight
from Bio.Seq import Seq
seq = Seq("ATCGATCGATCG")
print(f"GC content: {gc_fraction(seq):.2%}")
print(f"Molecular weight: {molecular_weight(seq, seq_type='DNA'):.2f} g/mol")
When a user asks about a specific Biopython task:
Example search patterns for reference files:
# Find information about specific functions
grep -n "SeqIO.parse" references/sequence_io.md
# Find examples of specific tasks
grep -n "BLAST" references/blast.md
# Find information about specific concepts
grep -n "alignment" references/alignment.md
Follow these principles when writing Biopython code:
Import modules explicitly
from Bio import SeqIO, Entrez
from Bio.Seq import Seq
Set Entrez email when using NCBI databases
Entrez.email = "[email protected]"
Use appropriate file formats - Check which format best suits the task
# Common formats: "fasta", "genbank", "fastq", "clustal", "phylip"
Handle files properly - Close handles after use or use context managers
with open("file.fasta") as handle:
records = SeqIO.parse(handle, "fasta")
Use iterators for large files - Avoid loading everything into memory
for record in SeqIO.parse("large_file.fasta", "fasta"):
# Process one record at a time
- Network operations and file parsing can fail
from Bio import Entrez, SeqIO
Entrez.email = "[email protected]"
# Fetch sequence
handle = Entrez.efetch(db="nucleotide", id="EU490707", rettype="gb", retmode="text")
record = SeqIO.read(handle, "genbank")
handle.close()
print(f"Description: {record.description}")
print(f"Sequence length: {len(record.seq)}")
from Bio import SeqIO
from Bio.SeqUtils import gc_fraction
for record in SeqIO.parse("sequences.fasta", "fasta"):
# Calculate statistics
gc = gc_fraction(record.seq)
length = len(record.seq)
# Find ORFs, translate, etc.
protein = record.seq.translate()
print(f"{record.id}: {length} bp, GC={gc:.2%}")
from Bio.Blast import NCBIWWW, NCBIXML
from Bio import Entrez, SeqIO
Entrez.email = "[email protected]"
# Run BLAST
result_handle = NCBIWWW.qblast("blastn", "nt", sequence)
blast_record = NCBIXML.read(result_handle)
# Get top hit accessions
accessions = [aln.accession for aln in blast_record.alignments[:5]]
# Fetch sequences
for acc in accessions:
handle = Entrez.efetch(db="nucleotide", id=acc, rettype="fasta", retmode="text")
record = SeqIO.read(handle, "fasta")
handle.close()
print(f">{record.description}")
from Bio import AlignIO, Phylo
from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor
# Read alignment
alignment = AlignIO.read("alignment.fasta", "fasta")
# Calculate distances
calculator = DistanceCalculator("identity")
dm = calculator.get_distance(alignment)
# Build tree
constructor = DistanceTreeConstructor()
tree = constructor.nj(dm)
# Visualize
Phylo.draw_ascii(tree)
Solution: This is just a warning. Set Entrez.email to suppress it.
Solution: Check that IDs/accessions are valid and properly formatted.
Solution: Verify file format matches the specified format string.
Solution: Ensure sequences are aligned before using AlignIO or MultipleSeqAlignment.
Solution: Use local BLAST for large-scale searches, or cache results.
Solution: Use PDBParser(QUIET=True) to suppress warnings, or investigate structure quality.
To locate information in reference files, use these search patterns:
# Search for specific functions
grep -n "function_name" references/*.md
# Find examples of specific tasks
grep -n "example" references/sequence_io.md
# Find all occurrences of a module
grep -n "Bio.Seq" references/*.md
Biopython provides comprehensive tools for computational molecular biology. When using this skill:
references/ directoryThe modular reference documentation ensures detailed, searchable information for every major Biopython capability.
try:
handle = Entrez.efetch(db="nucleotide", id=accession)
except HTTPError as e:
print(f"Error: {e}")
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Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.
Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.
Set up and use 1Password CLI (op). Use when installing the CLI, enabling desktop app integration, signing in (single or multi-account), or reading/injecting/running secrets via op.
CLI to manage emails via IMAP/SMTP. Use `himalaya` to list, read, write, reply, forward, search, and organize emails from the terminal. Supports multiple accounts and message composition with MML (MIME Meta Language).