Getting Started

Installation

pip install sgffp

Or with uv:

uv add sgffp

For development:

git clone https://github.com/merv1n34k/sgffp.git
cd sgffp
uv sync --dev

Requires Python 3.12+.

Read a File

from sgffp import SgffReader

sgff = SgffReader.from_file("plasmid.dna")

# Sequence
print(sgff.sequence.value[:50])   # first 50 bases
print(sgff.sequence.length)       # e.g. 5420
print(sgff.sequence.topology)     # "circular" or "linear"

# Features
for f in sgff.features:
    print(f"{f.name} ({f.type}) {f.start}-{f.end}")

# Primers
for p in sgff.primers:
    print(f"{p.name}: {p.sequence}")

Export to JSON

import json
from sgffp import SgffReader

sgff = SgffReader.from_file("plasmid.dna")

blocks_json = {str(k): v for k, v in sgff.blocks.items()}
output = {
    "cookie": {
        "type_of_sequence": sgff.cookie.type_of_sequence,
        "export_version": sgff.cookie.export_version,
        "import_version": sgff.cookie.import_version,
    },
    "blocks": blocks_json,
}

print(json.dumps(output, indent=2))

Or use the CLI:

sff parse plasmid.dna -o plasmid.json

Write Back

from sgffp import SgffReader, SgffWriter

sgff = SgffReader.from_file("plasmid.dna")

# Modify something
sgff.notes.description = "Updated plasmid"
sgff.features.find_by_name("GFP").name = "eGFP"

# Write to a new file
SgffWriter.to_file(sgff, "updated.dna")

Create from Scratch

Use the builder pattern to create a new SnapGene file without reading an existing one:

from sgffp import SgffObject, SgffWriter

sgff = (
    SgffObject.new("ATGCATGCATGCATGC", topology="circular")
    .add_feature("GFP", "CDS", 0, 8)
    .add_feature("AmpR", "CDS", 8, 16, strand="-")
    .add_primer("fwd", "ATGCATGC", bind_position=0)
)

sgff.notes.description = "My plasmid"

SgffWriter.to_file(sgff, "new_plasmid.dna")

SgffObject.new() accepts:

Parameter	Default	Options
sequence	""	DNA/RNA/protein string
topology	"linear"	"linear", "circular"
strandedness	"double"	"single", "double"
sequence_type	"dna"	"dna", "rna", "protein"

All builder methods (add_feature, add_primer, set_sequence) return self for chaining.