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 thepage.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.