unravel.allen_institute.genetic_tools_atlas.simplify_metadata module#
Use gta_simplify_metadata (gta_sm) from UNRAVEL to simplify metadata from the Genetic Tools Atlas (GTA).
- Prereqs:
Visit the GTA: https://portal.brain-map.org/genetic-tools/genetic-tools-atlas
Click “Access Genetic Tools Atlas”
Filter by ‘Data Modality’ = ‘STPT’
‘Download Data’ → ‘Metadata Table’
Unzip the downloaded file, find SpecimenMetadata.csv, and use it as the input.
Note
Default columns to keep: ‘Image Series ID’ ‘Donor Genotype’ ‘Vector Full Name’ ‘Targeted Cell Population’ ‘Cargo’ ‘Vector Delivery Method’
Duplicate rows in ‘Image Series ID’ are dropped.
The output file is saved as ‘SpecimenMetadata_subset.csv’ in the current directory.
If you want to keep other columns, use the -col option with a space-separated list of column names.
If you want to change the output file name, use the -o option.
- Next steps:
Run
gta_org_samples(gta_os) to organize the GTA data across samples for batch processing.
Usage:#
gta_sm -i “path/to/SpecimenMetadata.csv” [-col col1 col2 …] [-o output] [-v]