File size: 3,279 Bytes
e0036c5 | 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 | #!/usr/bin/env python3
"""Check status of data files required for reproducibility."""
import os
from pathlib import Path
def check_data_status():
repo_root = Path(__file__).parent.parent.parent
print("=" * 70)
print("Squidiff Reproducibility - Data Status Check")
print("=" * 70)
data_checks = [
# (description, path, required_for_figure)
("Fig 2: Differentiation", "datasets/ipsc_diff/log_normalised_counts.csv", "Fig 2"),
("Fig 3a-c: Gene Perturbation", "datasets/gears_train_data.h5ad", "Fig 3a-c"),
("Fig 3a-c: Gene Perturbation (test)", "datasets/gears_test_data.h5ad", "Fig 3a-c"),
("Fig 3d-g: GBM Drug Screening", "squidward_study/public_01/pub_all_data.h5ad", "Fig 3d-g"),
("Fig 4-6: Supplementary", "datasets/adata_norm.h5ad", "Fig 1 & Fig 3"),
]
status_symbols = {
'present': '✓',
'missing': '✗',
'partial': '⚠',
}
print("\nDATA FILE STATUS:\n")
total = len(data_checks)
available = 0
missing = []
for desc, path, figure in data_checks:
full_path = repo_root / path
if full_path.exists():
size = os.path.getsize(full_path) / (1024**3) # Convert to GB
symbol = status_symbols['present']
status = "Present"
available += 1
print(f"{symbol} {desc}")
print(f" → {path} ({size:.2f} GB)")
else:
symbol = status_symbols['missing']
status = "Missing"
missing.append((desc, path, figure))
print(f"{symbol} {desc}")
print(f" → {path}")
print()
# Summary
print("=" * 70)
print(f"SUMMARY: {available}/{total} datasets available")
print("=" * 70)
if missing:
print(f"\nMISSING DATA ({len(missing)} files):\n")
for desc, path, figure in missing:
print(f"• {desc} ({figure})")
print(f" Path: {path}")
if "GBM" in desc or "Fig 3d-g" in figure:
print(f" Download: See GBM_DATA_DOWNLOAD_GUIDE.md")
print(f" Source: GEO accession GSE148842")
print(f" Size: ~2.7 GB (compressed from series matrix)")
print()
# Recommendations
print("=" * 70)
print("RECOMMENDATIONS:\n")
if any("GBM" in d for d, _, _ in missing):
print("1. Download GBM data:")
print(" - Read: GBM_DATA_DOWNLOAD_GUIDE.md")
print(" - Run: python3 convert_series_matrix_to_h5ad.py (after download)")
print(" - Source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148842")
print()
if available > 0:
print(f"2. You can run figures that have complete data:")
available_figures = []
if (repo_root / "datasets/ipsc_diff/log_normalised_counts.csv").exists():
available_figures.append("Fig 2")
if (repo_root / "datasets/gears_train_data.h5ad").exists():
available_figures.append("Fig 3a-c")
if available_figures:
print(f" → {', '.join(available_figures)}")
print()
print("=" * 70)
return len(missing) == 0
if __name__ == "__main__":
all_present = check_data_status()
exit(0 if all_present else 1)
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