metahq-cli 1.0.0rc2

The meta-hq CLI.

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

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