data_loader — DataLoader

Loads the KillifishAtlas expression data and query DE result files.

File: src/data_loader.py
Test: unittests/test_data_loader.py

Atlas dataset

The Atlas contains 677 samples across 15 tissues at ages 47–163 days.

Property	Value
Genes	25,122
Samples	677
Tissues	Brain, Eye, SpinalCord, Heart, Lung, Liver, Gut, Fat, Kidney, Spleen, Muscle, Skin, Bone, Testis, Ovary
Age range	47–163 days

Methods

load_counts()

Loads the raw count matrix from data/GSE308970_rawcount_Atlas_allbatches_merged_v3.csv.

Returns a pd.DataFrame (genes × samples).

load_metadata()

Loads sample metadata from data/ExperimentDesign_allbatches_combined_v7.csv.

Columns: tissue, age_days, sex, batch.
Note: Ovary and Testis are harmonized to Gonad in some internal operations.

load_atlas()

Returns (counts, metadata) aligned to shared samples.

load_query_files()

Loads all query_data/*.xlsx DE result files. Returns a dict of DataFrames keyed by tissue + comparison.

summary()

Prints tissue/sex breakdown and age range to stdout.

Example

from src.data_loader import DataLoader

loader = DataLoader()
counts, meta = loader.load_atlas()
print(counts.shape)   # (25122, 677)
print(meta.dtypes)