FreePublished on GitHub

biopython

Route Biopython computational biology workflows across sequence objects, file formats, alignments, structures, web databases, BioSQL, motifs, restriction enzymes, and specialized modules.

The English summary is being prepared. Showing the original description.

VectorSpaceLab/AREX-Skill

See how to install

Files included (36)

SKILL.md4.5 KB
references/capability-map.md4.9 KB
references/repo-provenance.md1.7 KB
references/repo-routing-metadata.json414 B
references/troubleshooting.md4.7 KB
scripts/biopython_quick_smoke.py1.8 KB
sub-skills/alignment-search-and-phylogeny/references/alignment-search-workflows.md7.3 KB
sub-skills/alignment-search-and-phylogeny/references/phylo-reference.md5.9 KB
sub-skills/alignment-search-and-phylogeny/references/searchio-blast-reference.md7.4 KB
sub-skills/alignment-search-and-phylogeny/references/troubleshooting.md7.2 KB
sub-skills/alignment-search-and-phylogeny/scripts/alignment_phylo_smoke.py3.2 KB
sub-skills/alignment-search-and-phylogeny/SKILL.md2.6 KB
sub-skills/file-io-and-format-conversion/references/file-io-workflows.md8.8 KB
sub-skills/file-io-and-format-conversion/references/format-reference.md6.0 KB
sub-skills/file-io-and-format-conversion/references/troubleshooting.md6.5 KB
sub-skills/file-io-and-format-conversion/scripts/seqio_alignio_smoke.py4.4 KB
sub-skills/file-io-and-format-conversion/SKILL.md3.0 KB
sub-skills/sequence-objects-and-features/references/sequence-feature-api.md11.0 KB
sub-skills/sequence-objects-and-features/references/troubleshooting.md9.6 KB
sub-skills/sequence-objects-and-features/scripts/sequence_feature_smoke.py4.9 KB
sub-skills/sequence-objects-and-features/SKILL.md2.7 KB
sub-skills/specialized-analyses-and-graphics/references/motif-restriction-reference.md6.5 KB
sub-skills/specialized-analyses-and-graphics/references/specialized-workflows.md10.4 KB
sub-skills/specialized-analyses-and-graphics/references/troubleshooting.md9.0 KB
sub-skills/specialized-analyses-and-graphics/scripts/specialized_modules_smoke.py2.9 KB
sub-skills/specialized-analyses-and-graphics/SKILL.md3.9 KB
sub-skills/structural-bioinformatics/references/structure-api-reference.md12.1 KB
sub-skills/structural-bioinformatics/references/structure-workflows.md13.3 KB
sub-skills/structural-bioinformatics/references/troubleshooting.md12.0 KB
sub-skills/structural-bioinformatics/scripts/pdb_structure_smoke.py2.4 KB
sub-skills/structural-bioinformatics/SKILL.md4.1 KB
sub-skills/web-databases-and-biosql/references/biosql-reference.md5.6 KB
sub-skills/web-databases-and-biosql/references/troubleshooting.md7.4 KB
sub-skills/web-databases-and-biosql/references/web-database-workflows.md11.1 KB
sub-skills/web-databases-and-biosql/scripts/offline_database_parsers_smoke.py3.7 KB
sub-skills/web-databases-and-biosql/SKILL.md2.2 KB

SKILL.md (original)

Review the instructions the agent will receive before you install.

Biopython repo skill

Use this skill when a task asks for Biopython, Bio.*, BioSQL, or general computational-biology workflows that Biopython owns: sequences, biological file formats, alignments, BLAST/search output parsing, phylogenetic trees, macromolecular structures, public biological databases, motifs, restriction enzymes, and specialized bioinformatics modules.

First checks

Public install: python -m pip install biopython; conda users can install from conda-forge.
Source/developer install: python -m pip install -e . from a Biopython checkout when editing the package.
Required runtime dependency: NumPy. Optional features may need ReportLab, matplotlib, networkx, rdflib, database drivers, or external bioinformatics executables.
Minimal import check:

import Bio
from Bio.Seq import Seq
from Bio import SeqIO
print(Bio.__version__, Seq("ATGGCC").translate())

Run scripts/biopython_quick_smoke.py when you need a safe offline package smoke check before deeper work.
Read references/repo-provenance.md before deciding whether this skill is current for a checkout. If the commit, package version, or evidence paths differ substantially, refresh the skill.
Read references/troubleshooting.md for install/import/build issues, optional dependency failures, online-service constraints, and source-tree warning recovery.
Read references/capability-map.md when a request spans multiple Biopython modules or you need optional dependency ownership.

Route by task

User task	Read next	Notes
Create/manipulate `Seq`, `MutableSeq`, `SeqRecord`, annotations, features, locations, codon tables, reverse complements, translations, GC/protein utilities	sequence-objects-and-features	In-memory object semantics; route file parsing/writing onward to file I/O.
Parse, read, write, index, or convert FASTA/FASTQ/GenBank/EMBL/SwissProt/UniProt XML/alignment files	file-io-and-format-conversion	Covers `SeqIO`, `AlignIO`, low-level FASTA/FASTQ iterators, BGZF, `index`, `index_db`, and format names.
Pairwise/multiple alignments, substitution matrices, BLAST/SearchIO parsing, local or online BLAST result handling, phylogenetic tree I/O/traversal	alignment-search-and-phylogeny	For online BLAST policy, also read the web/database sub-skill.
PDB/mmCIF/BinaryCIF/PQR/PDBML structure parsing, SMCRA traversal, atom/residue selection, disordered atoms, contacts, geometry, superposition	structural-bioinformatics	External tools such as DSSP/NACCESS/MSMS are optional and not part of the base install.
Entrez, KEGG, UniProt, Swiss-Prot, ExPASy, GenBank, Medline, GEO, public-database parsers, qblast network etiquette, BioSQL	web-databases-and-biosql	Default to offline parsing examples; live services require user email/API policy and network handling.
Motifs, PWM/PSSM, JASPAR, restriction enzymes, clustering, phenotype arrays, GenePop/popgen, GenomeDiagram/graphics, SeqUtils/ProtParam, long-tail modules	specialized-analyses-and-graphics	Optional graphics/database integrations are documented but not required for base use.

Boundary rules

Do not use Biopython as a replacement for HTSlib-backed BAM/CRAM/VCF command wrappers; use dedicated HTS tools when the request needs samtools/bcftools/tabix semantics.
Do not claim online-service verification unless you actually ran the network call with user-approved email/API key/rate policy.
Do not require the original Biopython repository checkout for runtime guidance; this skill bundles the operating references and smoke scripts future agents need.
If a workflow needs an optional package, external executable, database server, or credentials, stop at the sub-skill troubleshooting section and ask for/verify that dependency before running live work.

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Install

Install with a command

npx skills add https://github.com/VectorSpaceLab/AREX-Skill --skill biopython

Paste it into your terminal and run it (requires Node.js). You can choose which agents to install it for, such as Claude Code or Codex.

Ask your agent

Please install the following Agent Skill.
https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/biopython

First review SKILL.md and the bundled files and confirm there is nothing suspicious (such as sending data externally or reading credentials). Then place it in ~/.claude/skills/biopython/ for Claude Code, or ~/.agents/skills/biopython/ for Codex.

Send this text to Claude Code or Codex as is. It checks the contents before installing.

View source on GitHub

Repository: VectorSpaceLab/AREX-Skill
Stars: 339
Forks: 26
Category: Development
License: Apache-2.0
Original language: English
Last updated: Sep 3, 2026

A skill is a set of instructions and scripts for an agent. cccskills does not guarantee that skills are safe. Review the contents before you install.