The meta-hq CLI.
Project description
A command line interface to query the MetaHQ database.
Key features
- Query standardized and harmonized biomedical annotations
- Access metadata for samples and studies in GEO and SRA
- Convert annotations to labels
- Fast execution time
- Search for relevant ontology terms with free-text queries
- Contribute new annotation sets to the database
Docs
Documentation: https://meta-hq.readthedocs.io/en/latest
Source Code: https://github.com/krishnanlab/meta-hq/tree/main/packages/cli
Installation and setup
To install:
pip install metahq-cli
Setup: This command must be run with every metahq-cli installation. The setup command downloads the
MetaHQ database from Zenodo.
metahq setup --doi latest
Retrieve
Query the MetaHQ database to retrieve sample or study annotations for tissues, diseases, sex, and age.
metahq retrieve diseases --terms "MONDO:0004994,MONDO:0008903" \
--level sample --filters "species=human,tech=rnaseq,ecode=expert" \
--metadata "sample,series,platform,srp" --fmt parquet
Search
If you do not have ontology terms memorized off-hand, shame on you. However, you can cheat and run the following command to find the ontology term IDs most similar to a free-text query of a disease, tissue, or cell line.
metahq search --query "heart attack" --type disease --ontology MONDO
Supported
Run the following to view supported attributes, filters, formats, etc.
metahq supported
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