Configuration and logging

Gene set libraries and configuration

page uses gene sets from Enrichr gene set libraries.

Enrichment of a few is performed by default but this can be customizable by the user.

The user can customize page in two ways:

• In a YAML file located in $HOME/.page.config.yaml;

• At run time with through the gene_set_libraries option in the page.page() function.

• At run time with the -g or --gene-set-libraries option if using the command-line interface.

The YAML configuration file is entirely optional, but does allow more flexibility and ease specically when selecting a large number of gene set libraries (each with its own gene sets).

To see which gene set libraries are available, go to https://amp.pharm.mssm.edu/Enrichr/#stats.

page does not need any static files with genes, but gets automatically what is needed and keeps a cache of what has been used in order to save API calls and greatly improve speed.

Logging

page will log its operations and errors using the Python standard logging library.

This will happen by default to standard output (sys.stdout) but also to a file in $HOME/.page.log.txt.

The location of the log file and the level of events to be reported can be customized in the page.setup_logger() function.