snapgene

name	snapgene
description	Parse SnapGene .dna files. Use when the user asks to read, convert, or extract information from SnapGene files, or needs to convert .dna to GenBank/FASTA format.

SnapGene Reader

Parse SnapGene .dna files and extract sequence, features, and metadata.

CLI Location

scripts/snapgene_cli.py

Dependencies

pip install snapgene_reader biopython

Commands

Show Summary

python3 scripts/snapgene_cli.py 438-C.dna

Output: name, length, feature count, topology

List Features

python3 scripts/snapgene_cli.py 438-C.dna --features

Output: table of all features (type, position, strand, name)

Print Sequence

python3 scripts/snapgene_cli.py 438-C.dna --sequence

Output: raw DNA sequence

Convert to GenBank

python3 scripts/snapgene_cli.py 438-C.dna --export-gb 438-C.gb

Convert to FASTA

python3 scripts/snapgene_cli.py 438-C.dna --export-fasta 438-C.fa

JSON Output

python3 scripts/snapgene_cli.py 438-C.dna --json

Output: full data as JSON (name, length, sequence, features with qualifiers)

Options

Option	Short	Description
--features	-f	List all features as table
--sequence	-s	Print DNA sequence only
--export-gb FILE	-g	Export to GenBank format
--export-fasta FILE	-a	Export to FASTA format
--json	-j	Output as JSON

Example Output

Summary

SnapGene File: 438-C.dna
==================================================
Name: 438-C
Length: 6,847 bp
Features: 24
Topology: circular

Feature types:
  CDS: 4
  misc_feature: 8
  promoter: 2
  rep_origin: 1
  terminator: 2

Features Table

Type            Start     End Strand Name
------------------------------------------------------------
promoter           1     300 +      polyhedrin promoter
CDS              500    2846 +      His6-MBP-TEV
misc_feature    2847    2864 +      LIC site
CDS             5000    5600 -      GentR

Integration

Use with construct generator to load vectors:

from snapgene_reader import snapgene_file_to_seqrecord

record = snapgene_file_to_seqrecord("438-C.dna")
sequence = str(record.seq)
features = record.features

Use with orf_verifier for clone verification:

# Convert vector to GenBank first
python3 scripts/snapgene_cli.py vector.dna --export-gb vector.gb

# Then verify clone
python3 scripts/orf_verifier_cli.py verify-clone --expected vector.gb --sequencing clone.seq