Routes 3D ResNets PyTorch video action-recognition workflows across training, inference, and data preparation.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
VectorSpaceLab/AREX-Skill3392026년 9월 3일 업데이트
무료GitHub에 공개
biopython
Route Biopython computational biology workflows across sequence objects, file formats, alignments, structures, web databases, BioSQL, motifs, restriction enzymes, and specialized modules.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
설치 방법 보기포함된 파일(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(원문)
설치하기 전에 에이전트에게 전달되는 지시 내용을 확인할 수 있습니다.
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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