Sequence & Features

SgffSequence

Wrapper for DNA, RNA, and Protein sequence blocks.

from sgffp import SgffSequence

BLOCK_IDS: (0, 1, 21, 32) — DNA, compressed DNA, protein, RNA

Properties

Property	Type	Description
value	str	Sequence string (settable)
length	int	Sequence length
topology	str	"linear" or "circular" (settable)
strandedness	str	"single" or "double" (settable)
is_circular	bool	True if circular topology
is_double_stranded	bool	True if double-stranded
block_id	int | None	Active block type (0, 1, 21, 32) (settable)
data	SgffSequenceData	Underlying dataclass

Setting value, topology, or strandedness automatically syncs back to the blocks dict.

SgffSequenceData

Underlying dataclass for sequence data.

Field	Type	Default
value	str	""
topology	str	"linear"
strandedness	str	"single"
dam_methylated	bool	False
dcm_methylated	bool	False
ecoki_methylated	bool	False

Methods: from_dict(data), to_dict(), property length.

---

SgffFeatureList

List model for annotation features. Inherits from SgffListModel[SgffFeature].

from sgffp import SgffFeatureList

BLOCK_IDS: (10,)

Methods

Method	Description
find_by_name(name) → SgffFeature | None	Find first feature by name
find_by_type(type_) → List[SgffFeature]	Find all features of a type
add(feature)	Add a feature and sync
remove(idx) → bool	Remove by index and sync
clear()	Remove all features
len(fl)	Count of features
fl[idx]	Feature at index
for f in fl	Iterate features

SgffFeature

Single annotation feature.

from sgffp import SgffFeature, SgffSegment

Field	Type	Default	Description
name	str		Feature name
type	str		Feature type (e.g., "CDS", "promoter")
strand	str	"+"	"+", "-", "." (none), "=" (both)
segments	List[SgffSegment]	[]	Location ranges
qualifiers	Dict[str, Any]	{}	Parsed qualifiers
color	str | None	None	Color from first segment
reading_frame	int | None	None	Reading frame offset (-3…-1, 1…3)
extras	Dict	{}	Unmodeled XML attributes
raw_qualifiers	List | None	None	Raw qualifier dicts for lossless roundtrip

Computed Properties

Property	Type	Description
start	int	First segment start (0-based)
end	int	Last segment end (1-based)

Methods

Method	Returns	Description
length(seq_len=None)	int	Feature length. For origin-spanning features on circular sequences, pass seq_len to get the correct wrapped length.
from_dict(data)	SgffFeature	Create from dict
to_dict()	Dict	Serialize to dict

SgffSegment

Single feature location range.

Field	Type	Default	Description
start	int		Start position (0-based)
end	int		End position (1-based)
color	str | None	None	Hex color (e.g., "#00ff00")
type	str	"standard"	Segment type: "standard" or "gap"
translated	bool	False	Whether this segment is translated
extras	Dict	{}	Unmodeled XML attributes

Methods: from_dict(data), to_dict().

---

SgffPrimerList

List model for primers. Inherits from SgffListModel[SgffPrimer].

from sgffp import SgffPrimerList

BLOCK_IDS: (5,)

Provides the same list operations as SgffFeatureList: add(), remove(), clear(), indexing, iteration.

SgffPrimer

Single primer definition.

from sgffp import SgffPrimer

Field	Type	Default	Description
name	str	""	Primer name
sequence	str	""	Primer sequence
binding_sites	List[SgffBindingSite]	[]	Parsed binding site data
extras	Dict	{}	Unmodeled XML attributes

Computed Properties (backward compatible)

Property	Type	Description
bind_position	int | None	Start position of first non-simplified binding site (0-based)
bind_strand	str	Strand of first non-simplified binding site ("+" or "-")
melting_temperature	float | None	Melting temperature of first non-simplified binding site

Methods

Method	Description
clear_binding_sites()	Remove all binding site data so SnapGene recalculates it
from_dict(data)	Create from parsed dict
to_dict()	Serialize to dict

SgffBindingSite

A single primer binding site on the target sequence. SnapGene stores both detailed and simplified versions of each site.

from sgffp import SgffBindingSite

Field	Type	Default	Description
start	int	0	Start position (0-based)
end	int	0	End position (1-based)
bound_strand	str	"+"	"+" (forward/top) or "-" (reverse/bottom)
annealed_bases	str	""	Annealed base sequence
melting_temperature	float | None	None	Melting temperature in °C
simplified	bool	False	Whether this is a simplified binding site
extras	Dict	{}	Unmodeled data (e.g., Component elements)

Methods

Method	Returns	Description
length(seq_len=None)	int	Binding site length. For origin-spanning sites on circular sequences, pass seq_len to get the correct wrapped length.
from_dict(data)	SgffBindingSite	Create from dict
to_dict()	Dict	Serialize to dict