Learn implied sample modifier in peppy

This vignette will show you how and why to use the implied attributes functionality of the peppy package.

• basic information about the PEP concept on the project website

• broader theoretical description in the implied attributes documentation section.

Problem/Goal

The example below demonstrates how and why to use implied attributes functionality to save your time and effort in case multiple sample attributes need to be defined for many samples and they follow certain patterns. Please consider the example below for reference:

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

sample_name  organism  time  file_path                        genome  genome_size
frog_0h      frog      0     data/lab/project/frog_0h.fastq
frog_1h      frog      1     data/lab/project/frog_1h.fastq
human_1h     human     1     data/lab/project/human_1h.fastq  hg38    hs
human_0h     human     0     data/lab/project/human_0h.fastq  hg38    hs
mouse_1h     mouse     1     data/lab/project/mouse_1h.fastq  mm10    mm
mouse_0h     mouse     0     data/lab/project/mouse_1h.fastq  mm10    mm

Solution

Noticeably, the samples with attributes human and mouse (in the organism column) follow two distinct patterns here. They have additional attributes in attributes genome and genome_size in the sample_table.csv file. Consequently you can use implied attributes to add those attributes to the sample annotations (set global, species-level attributes at the project level instead of duplicating that information for every sample that belongs to a species). The way how this process is carried out is indicated explicitly in the project_config.yaml file (presented below).

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

pep_version: '2.0.0'
sample_table: sample_table.csv
looper:
  output_dir: $HOME/hello_looper_results

sample_modifiers:
  imply:
    - if:
        organism: human
      then:
        genome: hg38
        macs_genome_size: hs
    - if:
        organism: mouse
      then:
        genome: mm10
        macs_genome_size: mm

Consequently, you can design sample_modifiers.imply - a multi-level key-value section in the project_config.yaml file. Note that the keys must match the column names and attributes in the sample_annotations.csv file.

Let's introduce a few modifications to the original sample_table.csv file to use the sample_modifiers.imply section of the config. Simply skip the attributes that will be implied and let the peppy do the work for you.

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

sample_name  organism  time  file_path
frog_0h      frog      0     data/lab/project/frog_0h.fastq
frog_1h      frog      1     data/lab/project/frog_1h.fastq
human_1h     human     1     data/lab/project/human_1h.fastq
human_0h     human     0     data/lab/project/human_0h.fastq
mouse_1h     mouse     1     data/lab/project/mouse_1h.fastq
mouse_0h     mouse     0     data/lab/project/mouse_1h.fastq

Code

Load 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_imply' (/Users/mstolarczyk/Uczelnia/UVA/code/peppy/tests/data/example_peps-cfg2/example_imply/project_config.yaml)
6 samples: frog_0h, frog_1h, human_1h, human_0h, mouse_1h, mouse_0h
Sections: pep_version, sample_table, looper, sample_modifiers

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 two last columns manually determined.