Other Models

SgffNotes

File-level metadata (block 6). Inherits from SgffModel.

from sgffp import SgffNotes

BLOCK_IDS: (6,)

Properties

Property	Type	Description
data	Dict	Raw notes dict
description	str	File description (settable)
created	str | None	Creation timestamp
last_modified	str | None	Last modification timestamp

Methods

Method	Description
get(key, default=None)	Get value by key
set(key, value)	Set value and sync
remove(key) → bool	Remove key and sync

Example

sgff.notes.description = "My plasmid"
sgff.notes.set("Type", "Synthetic")
print(sgff.notes.created)         # "2024-01-15.12:00:00"
sgff.notes.remove("CustomMapLabel")

---

SgffProperties

Sequence properties (block 8). Inherits from SgffModel.

from sgffp import SgffProperties

BLOCK_IDS: (8,)

Properties

Property	Type	Description
data	Dict	Raw properties dict

Methods

Method	Description
get(key, default=None)	Get value by key
set(key, value)	Set value and sync

Example

props = sgff.properties
print(props.get("UpstreamModification"))  # "Unmodified"
props.set("UpstreamStickiness", "4")

---

SgffAlignmentList

Alignable sequences (block 17). Inherits from SgffListModel[SgffAlignment].

from sgffp import SgffAlignmentList, SgffAlignment

BLOCK_IDS: (17,)

Provides standard list operations: add(), remove(), clear(), indexing, iteration.

SgffAlignment

Single alignable sequence.

Field	Type	Default	Description
name	str	""	Sequence name
sequence	str	""	Sequence string
extras	Dict	{}	Unmodeled attributes

Methods: from_dict(data), to_dict().

---

SgffTraceList

Chromatogram traces (block 16 containers). Inherits from SgffListModel[SgffTrace].

from sgffp import SgffTraceList

BLOCK_IDS: (16,)

Loads traces from block 16 containers — each container wraps a block 18 ZTR trace with optional block 8 properties. Block 18 never appears at the top level.

Provides standard list operations: add(), remove(), clear(), indexing, iteration.

SgffTrace

Single sequence trace (Sanger chromatogram).

from sgffp import SgffTrace

Field	Type	Default	Description
bases	str	""	Base calls
positions	List[int]	[]	Base-to-sample positions
confidence	List[int]	[]	Confidence scores per base
samples	SgffTraceSamples | None	None	ACGT channel intensities
clip	SgffTraceClip | None	None	Quality clip boundaries
text	Dict[str, str]	{}	Metadata key-value pairs
comments	List[str]	[]	Comment strings

Properties

Property	Type	Description
sequence	str	Alias for bases
length	int	Number of bases
sample_count	int	Number of sample points

Methods

Method	Description
get_metadata(key, default="")	Get metadata value
get_confidence_at(index) → int | None	Confidence at base index
get_position_at(index) → int | None	Sample position at base index
from_dict(data)	Create from parsed dict
to_dict()	Serialize to dict

SgffTraceClip

Quality clip boundaries.

Field	Type	Default	Description
left	int	0	Left clip position
right	int	0	Right clip position

SgffTraceSamples

Trace sample intensities for each channel.

Field	Type	Default	Description
a	List[int]	[]	Adenine channel
c	List[int]	[]	Cytosine channel
g	List[int]	[]	Guanine channel
t	List[int]	[]	Thymine channel

Property	Description
length	Number of sample points

Example

for trace in sgff.traces:
    print(f"{trace.length} bases, {trace.sample_count} samples")
    if trace.clip:
        print(f"  clip: {trace.clip.left}..{trace.clip.right}")
    if trace.samples:
        print(f"  A channel: {trace.samples.a[:5]}...")

---

SgffAttachmentList

File attachments (block 23). Inherits from SgffListModel[SgffAttachment].

from sgffp import SgffAttachmentList, SgffAttachment

BLOCK_IDS: (23,)

Provides standard list operations: add(), remove(), clear(), indexing, iteration. Additional lookup methods: get_by_name(name), get_by_id(file_id).

SgffAttachment

Single file attachment embedded in a SnapGene file.

Field	Type	Default	Description
id	int	0	File ID (auto-assigned on add)
name	str	""	Filename
data	bytes	b""	Raw file content
size	int	0	File size in bytes
mtime	str	""	Modification timestamp
compressible	str	"0"	Whether SnapGene may compress
extras	Dict	{}	Unmodeled manifest attributes

Methods: from_blocks(file_block, manifest_entry), to_manifest_dict(), to_file_block().

Example

for att in sgff.attachments:
    print(f"[{att.id}] {att.name}: {att.size} bytes")

sgff.add_attachment("gel.jpg", open("gel.jpg", "rb").read())
att = sgff.attachments.get_by_name("gel.jpg")

---

SgffTraceAlignment

Trace alignment data (block 27). Inherits from SgffModel. Contains BGZF-compressed BAM data — alignments of sequencing traces against the reference sequence.

from sgffp import SgffTraceAlignment, SgffBamRecord, SgffBamReference

BLOCK_IDS: (27,)

Property	Type	Description
header	str	SAM header text
references	List[SgffBamReference]	Reference sequences
records	List[SgffBamRecord]	Alignment records
record_count	int	Number of alignment records
reference_count	int	Number of reference sequences

SgffBamReference

Field	Type	Default	Description
name	str	""	Reference name
length	int	0	Reference length in bp

SgffBamRecord

Field	Type	Default	Description
read_name	str	""	Read/trace name (matches block 17 Sequence/@ID)
flag	int	0	SAM flag bits
ref_id	int	0	Reference sequence index
pos	int	0	0-based mapping position
mapq	int	255	Mapping quality
cigar	str	""	CIGAR string (e.g. 3S154M6S)
sequence	str	""	Read sequence
quality	List[int]	[]	Per-base quality scores

Properties: is_unmapped, is_reverse, length.

Example

if sgff.has_trace_alignment:
    ta = sgff.trace_alignment
    print(f"SAM header: {ta.header}")
    for ref in ta.references:
        print(f"  Reference: {ref.name} ({ref.length} bp)")
    for rec in ta.records:
        strand = "reverse" if rec.is_reverse else "forward"
        print(f"  {rec.read_name}: {strand}, CIGAR={rec.cigar}, {rec.length}bp")