evoseer-utils 0.2.0

Shared library for mutation management across modules

Mutation Library

Shared library for mutation management across modules.

Components

DbConnection - Singleton DB connection

from libs import DbConnection

DbConnection.set_db_path("mutations.db")
conn = DbConnection.get_connection()

Mutation - Pydantic model with DB integration

States

• "full": Has both id and (chrom, pos, ref, alt)
• "miss_id": Has coordinates, missing id
• "miss_attributes": Has id, missing coordinates

Creation patterns

# With coordinates (lazy load id)
mut = Mutation(chrom=17, pos=7577548, ref="C", alt="T")

# With id (lazy load attributes)
mut = Mutation(id=123)

# With both
mut = Mutation(id=123, chrom=17, pos=7577548, ref="C", alt="T")

Methods

Instance methods:

mut.fetch_id_from_db()           # Get id from coordinates
mut.fetch_attributes_from_db()   # Get coordinates from id
mut.ensure_in_db()              # Create if missing, return id

Class methods (batch):

Mutation.fetch_ids_from_db_batch(mutations)
Mutation.fetch_attributes_from_db_batch(mutations)
Mutation.ensure_in_db_batch(mutations)

Usage in modules with OutputDescription (fully automatic)

OutputDescription is a base class that provides automatic DB insertion for module outputs.

from pydantic import Field
from typing import ClassVar, List
from libs import OutputDescription, DbConnection, Mutation

class MyModuleOutput(OutputDescription):
    table_name: ClassVar[str] = "tool_mymodule"
    db_fields: ClassVar[List[str]] = ["my_score", "my_prediction"]

    my_score: float = Field(..., description="Module score")
    my_prediction: str = Field(..., description="Prediction")

# Setup
DbConnection.set_db_path("mutations.db")

# Single insertion (automatic table creation + mutation insertion)
output = MyModuleOutput(
    mutation=Mutation(chrom=17, pos=7577548, ref="C", alt="T"),
    version="1.0.0",  # Required field (free text)
    my_score=0.85,
    my_prediction="pathogenic"
)
output.insert_to_db()  # Creates table if needed, ensures mutation exists, inserts

# Batch insertion
outputs = [...]
MyModuleOutput.insert_batch_to_db(outputs)

What happens automatically:

• Table creation with correct SQL types (inferred from Python types)
• Mutation insertion/lookup
• Index creation on mutation_id
• version field automatically added to table and insertion
• INSERT OR REPLACE (idempotent)

Note: version field is required in all OutputDescription subclasses. Format is free text.

Chromosome encoding

• Autosomes: 1-22
• X: 23
• Y: 24

Helper functions:

from libs.src.mutations import chrom_to_int, int_to_chrom

chrom_to_int("chr17")  # 17
chrom_to_int("chrX")  # 23
int_to_chrom(23)  # "chrX"

Tests

# From project root
.venv/bin/python3 libs/tests/test_mutations_lib.py

# Or use the test runner
libs/tests/run_tests.sh

Examples

python3 example_mutations_lib.py
python3 modules/boostdm/output_description_example.py