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biopython

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

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VectorSpaceLab/AREX-Skill

查看安装方法

包含的文件（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（原文）

安装前可以查看交给 AI 代理的指令内容。

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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中文简介正在准备中。当前显示原文说明。