---

name: file-io-formats description: "Use Biotite to read, write, validate, and convert local sequence, structure, molecule, and trajectory file formats into Sequence, Annotation, AtomArray, and AtomArrayStack objects." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

File IO Formats

Use this sub-skill when a task is centered on biotite.sequence.io, biotite.structure.io, local parser classes, file round trips, or converting stored data into Biotite sequence, annotation, structure, molecule, or trajectory objects.

Route Here For

• FASTA, FASTQ, GenBank/GenPept, GFF3, Clustal, A3M, and generic sequence file loading/saving.
• PDB, PDBx/mmCIF, BinaryCIF, GRO, PDBQT, MOL, SDF, and generic structure file loading/saving.
• Choosing between PDBFile, CIFFile, BinaryCIFFile, MOLFile, SDFile, GROFile, and trajectory file classes.
• Using PDBx hierarchy objects: file, block, category, column, data, masks, BinaryCIF encodings, and compress().
• Converting files into Sequence, Annotation, Alignment, AtomArray, AtomArrayStack, BondList, and trajectory coordinate arrays.
• Debugging IO-specific failures such as text/binary handles, malformed records, missing trajectory templates, model/altloc choices, and unsupported fields.

Use Another Biotite Sub-skill For

• Sequence construction, alphabets, annotation analysis, alignments, profiles, and phylogeny after parsing: ../sequence-analysis/SKILL.md.
• AtomArray filtering, geometry, bonds, superposition, secondary structure, contacts, and trajectory analysis after loading: ../structure-analysis/SKILL.md.
• RCSB, Entrez, UniProt, PubChem, AlphaFold DB, BLAST, MSA wrappers, DSSP, SRA, Vina, and other network/external application planning: ../database-application/SKILL.md.
• PyMOL, RDKit, OpenMM, plotting, display, and visualization-oriented conversion: ../interfaces-visualization/SKILL.md.

Start With

1. Identify whether the input is sequence text, sequence annotations, an alignment, a coordinate structure, a small molecule, or a coordinate-only trajectory.
2. Prefer generic helpers (load_sequence(), load_sequences(), load_structure()) for simple extension-driven tasks; use format-specific file classes when options, metadata, annotations, bonds, models, or round-trip fidelity matter.
3. Choose text vs binary handles correctly: FASTA/FASTQ/GenBank/GFF/Clustal/PDB/CIF/MOL/SDF/GRO/PDBQT are text, BinaryCIF is binary, and trajectories usually require filesystem paths.
4. For structures, decide model, altloc, extra_fields, include_bonds, and author-vs-label fields before downstream analysis.
5. For trajectories, load a topology/template AtomArray or AtomArrayStack first; trajectory files normally store coordinates, boxes, and times, not atom annotations.

References

• API map and class chooser: references/api-reference.md.
• Format behavior and caveats: references/data-formats.md.
• Common local workflows: references/workflows.md.
• Failure recovery: references/troubleshooting.md.
• FASTA helper: scripts/roundtrip_sequence_io.py.
• PDB/PDBx helper: scripts/tiny_structure_io_smoke.py.

Quick Checks

From the Biotite skill root, run the no-network helpers when you need a local sanity check:

python sub-skills/file-io-formats/scripts/roundtrip_sequence_io.py
python sub-skills/file-io-formats/scripts/tiny_structure_io_smoke.py --mode pdb

Use --help on either helper for options. The structure helper intentionally focuses on tiny PDB/PDBx round trips; trajectory guidance is covered in the references because trajectory files are coordinate-only and require an external topology/template contract.