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FASTQ Format

Description​

FASTQ stores sequencing reads as four-line blocks: identifier, sequence, separator, and quality string. IterableData yields one dict per read with id, description, sequence, and quality. Registry id is fq (alias fastq). It is read-only in this release. Stdlib only — no optional dependency.

File Extensions​

  • .fq — FASTQ (registry id fq)
  • .fastq — common alias

Implementation Details​

Reading​

  • Parses classic four-line FASTQ blocks
  • @ header split into id and optional description
  • Skips incomplete trailing blocks
  • Streams from filename or text stream; supports encoding

Writing​

Writing is not supported.

Key Features​

  • Quality-aware reads: Phred ASCII quality string preserved as-is
  • Zero extras: base install only
  • Flat records: one dict per read

Usage​

from iterable import open_iterable

with open_iterable("reads.fq") as source:
    for rec in source:
        print(rec["id"], len(rec["sequence"]), rec["quality"][:10])

Parameters​

ParameterTypeDefaultRequiredDescription
encodingstrutf-8NoText encoding for the file

Installation​

pip install iterabledata

No format-specific extra.

Limitations​

  1. Read-only
  2. Classic 4-line blocks only (multi-line sequence/quality variants not supported)
  3. Does not validate that sequence and quality lengths match

Error Handling​

  • No ImportError for missing third-party deps
  • Format is registered writable=False
  • I/O errors: missing or unreadable files
  • Truncated files stop at the last complete block
  • FASTA — sequences without qualities
  • BAM / SAM — alignments