File size: 6,642 Bytes
99f834c | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 | """
Core mRNA sequence domain model.
Designed to be flexible: different databases store sequence data differently.
Some customers have a single 'mrna_sequence' field; others split into UTR/CDS/PolyA.
The SchemaMapper normalizes those into this model.
"""
from __future__ import annotations
import uuid
from dataclasses import dataclass, field
from typing import Any, Dict, List, Literal, Optional
@dataclass
class SequenceAnnotation:
"""A named region within a sequence (0-based, half-open [start, end))."""
label: str
start: int
end: int
strand: Literal["+", "-", "."] = "+"
color: Optional[str] = None
metadata: Dict[str, Any] = field(default_factory=dict)
@property
def length(self) -> int:
return self.end - self.start
@dataclass
class mRNASequence:
"""
Core mRNA sequence model.
Components are all optional because different databases represent
sequence data at different granularities. assembled_sequence will
concatenate whichever components are present, or return full_mrna
if the database provides the complete sequence as a single field.
"""
name: str
source: Literal["local", "database"]
# Auto-generated unique identifier
id: str = field(default_factory=lambda: str(uuid.uuid4()))
# Which database connection this came from (None for local sequences)
db_source: Optional[str] = None
# ── Sequence components (all optional) ──────────────────────────────────
# Stored as DNA (T not U) for computational convenience; displayed as RNA
five_prime_utr: Optional[str] = None
kozak: Optional[str] = None
cds: Optional[str] = None
three_prime_utr: Optional[str] = None
poly_a: Optional[str] = None
# Full pre-assembled sequence from DB (when component breakdown is unavailable)
full_mrna: Optional[str] = None
# Annotations populated by analysis or DB import
annotations: List[SequenceAnnotation] = field(default_factory=list)
# Raw database record — all original fields preserved for model use
raw_metadata: Dict[str, Any] = field(default_factory=dict)
# Analysis cache — populated lazily by SequenceAnalyzer
_analysis_cache: Dict[str, Any] = field(default_factory=dict, repr=False)
# ── Derived properties ──────────────────────────────────────────────────
@property
def assembled_sequence(self) -> str:
"""
Return the full sequence by concatenating present components.
Falls back to full_mrna if no components are set.
Raises ValueError if neither is available.
"""
parts = [
self.five_prime_utr or "",
self.kozak or "",
self.cds or "",
self.three_prime_utr or "",
self.poly_a or "",
]
assembled = "".join(parts)
if assembled:
return assembled.upper()
if self.full_mrna:
return self.full_mrna.upper()
raise ValueError(
f"Sequence '{self.name}' has no components and no full_mrna set."
)
@property
def has_components(self) -> bool:
"""True if at least one sub-component is explicitly set."""
return any([
self.five_prime_utr,
self.kozak,
self.cds,
self.three_prime_utr,
self.poly_a,
])
@property
def component_annotations(self) -> List[SequenceAnnotation]:
"""
Auto-derive position annotations from the component breakdown.
Only available when has_components is True.
"""
annotations = []
pos = 0
component_colors = {
"5'UTR": "#4A90D9",
"Kozak": "#F5A623",
"CDS": "#7ED321",
"3'UTR": "#9B59B6",
"PolyA": "#E74C3C",
}
components = [
("5'UTR", self.five_prime_utr),
("Kozak", self.kozak),
("CDS", self.cds),
("3'UTR", self.three_prime_utr),
("PolyA", self.poly_a),
]
for label, seq in components:
if seq:
annotations.append(SequenceAnnotation(
label=label,
start=pos,
end=pos + len(seq),
color=component_colors.get(label),
))
pos += len(seq)
return annotations
@property
def length(self) -> int:
try:
return len(self.assembled_sequence)
except ValueError:
return 0
@property
def cds_length(self) -> Optional[int]:
return len(self.cds) if self.cds else None
# ── Mutation helpers ────────────────────────────────────────────────────
def with_cds(self, cds: str) -> "mRNASequence":
"""Return a new mRNASequence with the CDS replaced."""
from dataclasses import replace
return replace(
self,
id=str(uuid.uuid4()),
cds=cds.upper(),
source="local",
db_source=None,
_analysis_cache={},
)
def to_dict(self) -> Dict[str, Any]:
return {
"id": self.id,
"name": self.name,
"source": self.source,
"db_source": self.db_source,
"five_prime_utr": self.five_prime_utr,
"kozak": self.kozak,
"cds": self.cds,
"three_prime_utr": self.three_prime_utr,
"poly_a": self.poly_a,
"full_mrna": self.full_mrna,
"raw_metadata": self.raw_metadata,
}
@classmethod
def from_dict(cls, data: Dict[str, Any]) -> "mRNASequence":
return cls(
id=data.get("id", str(uuid.uuid4())),
name=data["name"],
source=data.get("source", "local"),
db_source=data.get("db_source"),
five_prime_utr=data.get("five_prime_utr"),
kozak=data.get("kozak"),
cds=data.get("cds"),
three_prime_utr=data.get("three_prime_utr"),
poly_a=data.get("poly_a"),
full_mrna=data.get("full_mrna"),
raw_metadata=data.get("raw_metadata", {}),
)
def __repr__(self) -> str:
length = self.length
return f"mRNASequence(name={self.name!r}, source={self.source!r}, length={length})"
|