Cell Browser scripts

h5adMetaInfo

This script prints out a summary of the metadata in an h5ad file. Specifically, it prints out the unique values for each metadata column header field and the total number of unique values for each column of the metadata file.

To use this tool, you will need to be in your Scanpy environment:

h5adMetaInfo -f [number of fields to display] h5ad

rdsMetaInfo

This script is similar to the one above however it prints out a summary of the metadata for an rds file.

To use this tool, you will need to be in your Seurat environment:

rdsMetaInfo -f [number of fields to display] rds

Both scripts were developed in order to get a glance at the information stored in metadata files. These scripts save time in loading the files into either Python or R depending on the file type and extracting the data using a series of commands. Ultimately, this reduces typing the same commands over again. These scripts were inspired by Jim’s useful tool “tabInfo” which prints out a summary of the metadata in a tsv file.