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