CLI Reference

The sff command-line tool provides utilities for inspecting and manipulating SnapGene .dna files.

sff --version          # show version
sff <command> --help   # command-specific help

All read commands accept stdin by default — omit the input argument or pass - explicitly.

sff parse

Export a SnapGene file to JSON.

sff parse [input] [-o OUTPUT]

Argument	Description
input	Input .dna file (default: stdin)
-o, --output	Write JSON to file instead of stdout

Examples

sff parse plasmid.dna                     # print JSON to stdout
sff parse plasmid.dna -o plasmid.json     # write to file
cat plasmid.dna | sff parse               # read from stdin

---

sff info

Show file information summary.

sff info [input] [-v]

Argument	Description
input	Input .dna file (default: stdin)
-v, --verbose	Show detailed contents

Output

Basic mode shows: file type, sequence length/topology/strandedness, feature/primer/trace/history counts, block IDs present.

Verbose mode (-v) additionally shows: notes (description, created, modified), feature list with strand/type/positions, primer list, trace details, history tree.

Examples

sff info plasmid.dna
# File: plasmid.dna
# Type: DNA (export v15, import v19)
# Sequence: 5420 bp, circular, double-stranded
# Features: 12
# Primers: 4
# History: 3 nodes
# Blocks: 0, 5, 6, 7, 8, 10, 11

sff info -v plasmid.dna
# ... (includes feature list, primer list, history tree)

---

sff tree

Display the history tree in timeline order (chronological, leaves first).

sff tree [input] [-v]

Argument	Description
input	Input .dna file (default: stdin)
-v, --verbose	Show operation details (enzymes, oligos)

Output

Leaf nodes show as plain entries. Non-leaf nodes show the operation arrow. Resurrectable nodes are marked.

sff tree cloned.dna
#   [0] Vector.dna (4000bp, circular) [resurrectable]
#   [1] Insert.dna (1000bp, linear) [resurrectable]
#   └── insertFragment → [2] Final.dna (5000bp, circular)

Verbose mode shows InputSummary details (enzyme names, site counts) and oligo sequences.

---

sff check

Detect unknown block types. Silent by default.

sff check [input] [-l] [-d]

Argument	Description
input	Input .dna file (default: stdin)
-l, --list	List all block types found
-d, --dump	Dump hex data of unknown blocks

Examples

sff check plasmid.dna -l
#  0:  1
#  3:  1
#  6:  1
# 10:  1
# 13:  1

sff check plasmid.dna -l -d
# (also dumps hex of any blocks not in SCHEME)

Unknown blocks are marked with [NEW].

---

sff filter

Keep specific blocks and write a new file.

sff filter <input> -k KEEP -o OUTPUT

Argument	Description
input	Input .dna file (required)
-k, --keep	Comma-separated block type IDs to keep (required)
-o, --output	Output .dna file (required)

Examples

# Keep only sequence and features
sff filter plasmid.dna -k 0,10 -o minimal.dna

# Keep sequence, features, and notes
sff filter plasmid.dna -k 0,6,10 -o stripped.dna