The PEP filters are an experimental feature and may change in feature versions of
Eido provides a CLI to convert a PEP into different output formats. These include some built-in formats, like csv (which takes your spits out a processed csv file, with project/sample modified), yaml, and a few others. It also provides a plugin system so that you can write your own Python functions to provide custom output formats.
View available filters
Run this command to see what filters are available:
You'll see some output like this. There are a few built-in filters available:
Available filters: - basic - csv - yaml - yaml-samples
You can also write a custom filters, which will write your PEP into whatever format you need.
Convert a PEP into an alternative format with a filter
To convert a PEP into an output format, do this:
eido convert config.yaml -f basic running plugin pep Project 'pepconvert' (/home/nsheff/code/pepconvert/config.yaml) 5 samples: WT_REP1, WT_REP2, RAP1_UNINDUCED_REP1, RAP1_UNINDUCED_REP2, RAP1_IAA_30M_REP1 Sections: pep_version, sample_table, subsample_table ...
This basic format just lists the config file, the number of samples and their names, and identifies the sections in the project config file. Another format is
eido convert config.yaml -f yaml
This will output your samples in yaml format.
Parametrizing PEP conversions
The filter functions are parameterizable, so depending on the desired filter function design and required arguments you might need to provide them like this:
eido convert config.yaml -f yaml -a argument1=value1 argument2=value2