EvoPPI Querier

The pegi3s/evoppi-querier Docker image allows making queries to the EvoPPI web server.

Single species

The main script is query_single_species, so you should adapt and run the following command:

docker run --rm -v /your/data/dir:/data -w /data pegi3s/evoppi-querier query_single_species -c config.txt -o output_dir

In this command, you should replace:

/your/data/dir to point to the directory that contains the file you want to process.
config.txt to the actual name of your input TXT file with the configuration parameters (see below).
output_dir to the actual name of your output directory.

The script help can be obtained with docker run --rm pegi3s/evoppi-querier query_single_species --help.

Configuration parameters

These are the configuration parameters that must be included in the configuration text file:

Species=Homo sapiens
GeneID=411
Int_level=1
Format=single
Interactome.Databases=BioGRID; HIPPIE
Interactome.Modifiers_22=Homo sapiens (Modifiers_22)
Interactome.polyQ_22=Homo sapiens (PolyQ_22)
Predictome.Databases=Based on Drosophila melanogaster BioGRID (DIOPT); Based on Drosophila melanogaster BioGRID (ENSEMBL)
Predictome.Modifiers_22=
Predictome.polyQ_22=Homo sapiens Danio rerio (from DIOPT) (PolyQ_models_22)

Note that:

The names of the Species supported can be obtained with the following command: docker run --rm pegi3s/evoppi-querier list_species.
The names of the interactomes for the Interactome.* parameters can be obtained with the following command: docker run --rm pegi3s/evoppi-querier list_interactomes --species <Species> -dt interactome.
The names of the predictomes for the Predictome.* parameters can be obtained with the following command: docker run --rm pegi3s/evoppi-querier list_interactomes --species <Species> -dt predictome.
All parameters are mandatory, otherwise the program will not run. Interactome.* and Predictome.* may be empty and at least one itneractome/predictome name must be provided.

Test data

To test the query_single_species script, start creating a new file named config.txt with the previous example configuration. And then run the following command:

docker run --rm -v "$(pwd):$(pwd)" -w "$(pwd)" pegi3s/evoppi-querier query_single_species -c config.txt -o output_dir

The result will be available in the new output_dir directory created at your current working directory. As Format=single, this directory will contain a single file named EvoPPI_Results.csv.

Changelog

The latest tag contains always the most recent version.

[1.0.1] - 24/01/2024

Fixes a bug when retrieving query results that caused the first ten interactions were missing.

[1.0.0] - 22/01/2024

Initial pegi3s/evoppi-querier version containing the query_single_species script.