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Learn append sample modifier in peppy

This vignette will show you how and why to use the append functionality of the pepr package.

Problem/Goal

The example below demonstrates how to use the constant attributes to define the samples attributes in the read_type column of the sample_table.csv file. This functionality is extremely useful when there are many samples that are characterized by identical values of certain attribute (here: value SINGLE in read_type attribute). Please consider the example below for reference:

examples_dir = "../tests/data/example_peps-cfg2/example_append/"
sample_table_ori = examples_dir + "sample_table_pre.csv"
%cat $sample_table_ori | column -t -s, | cat

sample_name  organism  time  read_type

pig_0h       pig       0     SINGLE

pig_1h       pig       1     SINGLE

frog_0h      frog      0     SINGLE

frog_1h      frog      1     SINGLE

Solution

As the name suggests the attributes in the specified attributes (here: read_type) can be defined as constant ones. The way how this process is carried out is indicated explicitly in the project_config.yaml file (presented below). The name of the column is determined in the sample_modifiers.append key-value pair. Note that definition of more than one constant attribute is possible.

project_config_file = examples_dir + "project_config.yaml"
%cat $project_config_file

pep_version: "2.0.0"
sample_table: sample_table.csv

sample_modifiers:
  append:
    read_type: SINGLE

Let's introduce a few modifications to the original sample_table.csv file to use the sample_modifiers.append section of the config. Simply skip the attributes that are set constant and let the pepr do the work for you.

sample_table = examples_dir + "sample_table.csv"
%cat $sample_table | column -t -s, | cat

sample_name  organism  time

pig_0h       pig       0

pig_1h       pig       1

frog_0h      frog      0

frog_1h      frog      1

Code

Import peppy and read in the project metadata by specifying the path to the project_config.yaml:

from peppy import Project
p = Project(project_config_file)

And inspect it:

print(p)
p.sample_table

Project 'example_append' (/Users/mstolarczyk/Uczelnia/UVA/code/peppy/tests/data/example_peps-cfg2/example_append/project_config.yaml)
4 samples: pig_0h, pig_1h, frog_0h, frog_1h
Sections: pep_version, sample_table, sample_modifiers
organism read_type sample_name time
sample_name
pig_0h pig SINGLE pig_0h 0
pig_1h pig SINGLE pig_1h 1
frog_0h frog SINGLE frog_0h 0
frog_1h frog SINGLE frog_1h 1

As you can see, the resulting samples are annotated the same way as if they were read from the original annotations file with attributes in the last column manually determined.