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.