Module outputs

Descriptive Tables for Predicted Modules

To describe predicted modules, various files can be generated, each describing different characteristics of these modules.

To generate these tables, use the write_pangenome command with the --module :

ppanggolin write_pangenome -p pangenome.h5 --modules -o my_output_dir

This command generates three tables: functional_modules.tsv, modules_in_genomes.tsv, and modules_summary.tsv described below:

1. Gene Family to Module Mapping Table

The functional_modules.tsv file lists modules with their corresponding gene families. Each line establishes a mapping between a gene family and its respective module.

It follows the following format:

Column	Description
module_id	Identifier for the module
family_id	Identifier for the family

2. Genome-wise Module Composition

The modules_in_genomes.tsv file provides a comprehensive overview of the modules present in each genome, detailing their completeness levels. Due to potential variability in module predictions, some modules might exhibit partial completeness in specific genomes where they are detected.

The structure of the modules_in_genomes.tsv file is outlined as follows:

Column	Description
module_id	Identifier for the module
genome	Genome in which the indicated module is found
completion	Indicates the level of completeness (0.0 to 1.0) of the module in the specified genome based on gene family representation

3. modules summary

The modules_summary.tsv file lists characteristics for each detected module, with one line for each module.

The format is as follows:

column	description
module_id	The module identifier
nb_families	The number of families which are included in the module The families themselves are listed in the ‘functional_modules.tsv’ file.
nb_genomes	The number of genomes in which the module is found. Those genomes are listed in the ‘modules_in_genomes.tsv’ file.
partition	The average partition of the families in the module.
mean_number_of_occurrence	the mean number of time a module is present in each genome. The expected value is around one, but it can be more if it is a module often repeated in the genomes (like a phage).

Mapping Modules with Spots and Regions of Genomic Plasticity (RGPs)

Predicted modules can be associated with Spots of insertion and Regions of Genomic Plasticity (RGPs) using the write_pangenome command with the --spot_modules flag as follows:

ppanggolin write_pangenome -p pangenome.h5 --spot_modules -o my_output_dir

This command generates two tables: modules_spots.tsv and modules_RGP_lists.tsv, described below.

Note

These outputs are available only if modules, spots, and RGPs have been computed in your pangenome (see the command all or the commands spot, rgp, and module for that).

Moreover, this information can be visualized through figures using the command ppanggolin draw --spots (refer to Spot plots, which can display modules).

1. Associating Modules and Spots

The modules_spots.tsv file indicates which modules are present in each spot.

Its format is as follows:

Column	Description
module_id	Module identifier
spot_id	Spot identifier

2. Associating Modules and RGPs

The modules_RGP_lists.tsv file lists RGPs that contain the same modules. These RGPs may have different gene families, but they will not include any other modules apart from those indicated. The format of modules_RGP_lists.tsv is as follows:

Column	Description
representative_RGP	An RGP considered representative for the group, serving as a randomly chosen ‘group of RGP IDs’
nb_spots	The number of spots where the RGPs containing the listed modules are observed
mod_list	A list of modules present in the indicated RGPs
RGP_list	A list of RGPs that specifically includes the previously listed modules

Module Information

Once module have been predicted, the info command can present overall statistics regarding the predicted modules, including details about the families found within the modules and their distribution across various partitions.

ppanggolin info -p pangenome.h5 --content

The command output provides the following details about modules:

[...]
Modules:
	Number_of_modules: 380
	Families_in_Modules: 2242
	Partition_composition:
		Persistent: 0.27
		Shell: 37.69
		Cloud: 62.04
	Number_of_Families_per_Modules:
		min: 3
		max: 65
		sd: 5.84
		mean: 5.9