Internals

SCHEME Dict

The SCHEME dictionary in sgffp.parsers maps block type IDs to parser functions. This is the central dispatch table used by parse_blocks().

from sgffp.parsers import SCHEME

Block ID	Parser	Content
0	parse_sequence	DNA sequence
1	parse_compressed_dna	2-bit compressed DNA
5	parse_xml	Primers (XML)
6	parse_xml	Notes (XML)
7	parse_lzma_xml	History tree (LZMA XML)
8	parse_xml	Sequence properties (XML)
10	parse_features	Features (XML + qualifier extraction)
11	parse_history_node	History node (binary)
14	parse_xml	Custom enzyme sets (XML)
16	parse_trace_container	Trace container (flags + nested TLV)
17	parse_xml	Alignable sequences (XML)
18	parse_ztr	ZTR trace data (inside block 16)
20	parse_xml	Strand colors (XML)
21	parse_sequence	Protein sequence
28	parse_xml	Enzyme visibilities (XML)
29	parse_lzma_xml	History modifier (LZMA XML)
30	parse_lzma_nested	History node content (LZMA nested TLV)
32	parse_sequence	RNA sequence
34	parse_lzma_json	RNA structure predictions (LZMA JSON)

Blocks not in SCHEME (2, 3, 13) are skipped — SnapGene regenerates them on import.

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Parser Functions

All parsers accept data: bytes and return a parsed dict (or None on failure).

parse_blocks(stream) → Dict[int, List[Any]]

Read TLV blocks from a binary stream and dispatch each to its SCHEME parser. Returns the top-level blocks dict used by SgffObject.

parse_sequence(data) → Dict

Parse uncompressed sequence (blocks 0, 21, 32). Returns:

{
    "sequence": str,
    "length": int,
    "topology": "linear" | "circular",
    "strandedness": "single" | "double",
    "dam_methylated": bool,
    "dcm_methylated": bool,
    "ecoki_methylated": bool,
}

parse_compressed_dna(data) → Dict

Parse 2-bit GATC-encoded DNA (block 1). Returns sequence plus metadata header fields (format_version, strandedness_flag, property_flags, header_seq_length).

parse_xml(data) → Dict | None

Parse XML block via xmltodict with clean JSON keys (strips @ prefixes, converts #text to _text).

parse_lzma_xml(data) → Dict | None

Decompress LZMA, then parse XML.

parse_lzma_json(data) → Any | None

Decompress LZMA, then parse JSON.

parse_lzma_nested(data) → Dict[int, List] | None

Decompress LZMA, then parse as nested TLV blocks.

parse_features(data) → Dict | None

Parse feature XML with qualifier extraction and strand mapping. Returns:

{
    "features": [{"name": str, "type": str, "strand": str, "start": int, "end": int, ...}],
    "wrapper_extras": {"nextValidID": str, ...},
}

parse_ztr(data) → Dict | None

Parse ZTR-format Sanger sequencing trace. Handles chunks: BASE, BPOS, CNF4, SMP4, SAMP, TEXT, CLIP, COMM. Supports raw (format 0) and zlib (format 2) compression.

parse_trace_container(data) → Dict

Parse block 16: 4-byte flags header + nested TLV blocks.

parse_history_node(data) → Dict

Parse block 11 binary: node_index, sequence_type, sequence data, nested TLV blocks.

octet_to_dna(raw_data, base_count) → bytes

Convert 2-bit encoded bytes to ASCII DNA. Encoding: G=00, A=01, T=10, C=11.

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SgffModel

Base class for all block-backed models.

from sgffp.models.base import SgffModel

Member	Description
BLOCK_IDS	Tuple of relevant block type IDs
exists → bool	True if any relevant blocks exist

Protected Helpers

Method	Description
_get_block(block_id) → Any | None	Get first item from block
_set_block(block_id, value)	Set block value (replaces)
_get_blocks(block_id) → List	Get all items from block
_set_blocks(block_id, values)	Set all block values
_remove_block(block_id) → bool	Remove block entirely

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SgffListModel[T]

Generic base for list-backed models. Extends SgffModel.

from sgffp.models.base import SgffListModel

Member	Description
items → List[T]	Lazily loaded item list
add(item)	Append item and sync
remove(idx) → bool	Remove by index and sync
clear()	Remove all items and sync
len(model)	Item count
model[idx]	Item at index
for item in model	Iterate items

Abstract Methods (subclass must implement)

Method	Description
_load() → List[T]	Parse items from block storage
_sync()	Write items back to block storage

Subclasses

• SgffFeatureList (block 10)
• SgffPrimerList (block 5)
• SgffAlignmentList (block 17)
• SgffTraceList (block 16)