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PEPkit

Basic PEP example

This vignette will show you a simple example PEP-formatted project, and how to read it into python using the peppy package. This example comes from the example_peps repsitory in the example_basic folder.

Start by importing peppy, and then let's take a look at the configuration file that defines our project:

import peppy
examples_dir = "../tests/data/example_peps-cfg2/"
project_config_file = examples_dir + "example_basic/project_config.yaml"
%cat $project_config_file
pep_version: "2.0.0"
sample_table: sample_table.csv

It's a basic YAML-formatted file with couple of sections:

  • pep_version (required; indicates with PEP spec version this config subscribes to)
  • sample_table (suggested; a pointer to sample annotation sheet. It is stored in the same folder as project_config.yaml)

Now, let's now glance at that annotation file:

sample_table = examples_dir + "example_basic/sample_table.csv"
%cat $sample_table | column -t -s, | cat
sample_name  protocol       file
frog_1       anySampleType  data/frog1_data.txt
frog_2       anySampleType  data/frog2_data.txt

This sample_table.csv file is a basic CSV file, with rows corresponding to samples, and columns corresponding to sample attributes. Let's read this simple example project into Python using peppy:

project = peppy.Project(examples_dir + "example_basic/project_config.yaml")

Now, we have access to all the project metadata in easy-to-use form using python objects. We can browse the samples in the project like this:

project.samples[0].file
'data/frog1_data.txt'