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FASTA Format

Description​

FASTA is a text format for biological sequences (DNA, RNA, protein). IterableData streams one record per sequence header with id, description, and sequence. Registry id is fa (aliases: fasta, fna, faa). It is read-only in this release. No optional dependency — stdlib only.

File Extensions​

  • .fa — FASTA (registry id fa)
  • .fasta — common alias
  • .fna — nucleic acid FASTA alias
  • .faa — amino acid FASTA alias

Implementation Details​

Reading​

  • Line-oriented parser: > headers start a new record
  • Header split into first token (id) and remainder (description)
  • Sequence lines are concatenated (blank lines skipped)
  • Streams from filename or text stream; supports encoding

Writing​

Writing is not supported.

Key Features​

  • Streaming sequences: does not require loading the whole file as a single string
  • Zero extras: no pip optional beyond base iterabledata
  • Flat records: one dict per sequence

Usage​

from iterable import open_iterable

with open_iterable("genes.fa") as source:
    for rec in source:
        print(rec["id"], len(rec["sequence"]), rec.get("description"))

Parameters​

ParameterTypeDefaultRequiredDescription
encodingstrutf-8NoText encoding for the file

Installation​

pip install iterabledata

No format-specific extra.

Limitations​

  1. Read-only
  2. Multi-line quality / wrapped formats other than classic FASTA are not handled
  3. Very large single sequences still allocate the full sequence string in memory per record

Error Handling​

  • No ImportError for missing third-party deps (stdlib parser)
  • Write mode does not produce records; format is registered writable=False
  • I/O errors: missing or unreadable files
  • Malformed files may yield incomplete last records or skip empty content