SnapGene .dna: reading and writing

DNAgent reads SnapGene files and writes them, so a construct can go out to a lab that works in SnapGene without an import step. Source files are never modified in place: writing always goes to a path you choose.

Two ways a file is written

Verbatim. A record that DNAgent read from .dna and has not edited since is written back byte for byte — the same cookie version fields, the same sequence flag bits, the same packet order, and the annotation packets as their original XML. Nothing SnapGene stores is lost by passing a file through DNAgent, including the packets DNAgent does not interpret.

Before copying those packets, DNAgent re-reads them and compares them with the record. If they no longer agree, it does not copy them: a file whose annotation packets contradict its own model would be worse than no file.

Generated. Anything else — an edited record, a Gibson product, a construct read from GenBank or FASTA — has its Features and Primers packets built from DNAgent's model. Such a file holds exactly what DNAgent models and is reported as generated. It does not carry:

• the uninterpreted packets of a source file (0x03, 0x08, 0x0d, 0x0e, 0x11, 0x23, 0x1c, notes 0x06), because their meaning is unknown and they may describe annotations the record no longer has; each is named in a warning;
• SnapGene's display and detection attributes (translationMW, maxRunOn, detectionMode, allowSegmentOverlaps, …), which DNAgent does not model.

Sequence flag bits other than topology (methylation and similar settings) are carried over when the record came from a SnapGene file that set them, and reported.

Writing one

dnagent convert construct.gb --out construct.dna      # the extension chooses the format
dnagent annotate construct.dna --out annotated.dna --add --range 100..160 --label probe
dnagent gibson-optimise plan.json --out product.dna   # hand the product to a SnapGene lab

In the desktop app, Save as… offers SnapGene alongside GenBank; the status line says which format was written and repeats any warning.

What is checked

• Every valid public fixture, and (opt-in, via DNAGENT_PRIVATE_DNA) real SnapGene files, are read and written back byte for byte.
• Taken the long way round — .dna → DNAgent GenBank → .dna, which forces regeneration — Biopython 1.85, which never sees DNAgent's own reader, finds the same sequence, topology and features in the rebuilt file as DNAgent models in the original (scripts/check_snapgene_write.py).
• A record whose annotations no longer match its source packets is refused the verbatim path, and the desktop save reports the regeneration.

Opening a generated file in SnapGene itself is the acceptance test these cannot replace.