How to Use the PPIFormer

To extract the contents of the "PPIFormer.tar.gz" file in Linux, you can follow these steps:

1: Navigate to the directory where the "PPIFormer.tar.gz" file is located. For example, if the file is in the "Downloads" folder, you can use the following command:

                    
                        cd ~/Downloads
                    
                

2: Use the following command to extract the contents of the tar.gz file

                    
                        tar -xzf PPIFormer.tar.gz
                    
                

This command will extract the files and directories from the archive.

3: Once the extraction is complete, you can access the extracted files and use them as needed.

Please note that the exact steps may vary depending on your Linux distribution and the location of the tar.gz file.

Arguments

The View script is designed to analyze pathogen-host protein-protein interactions. Here's a breakdown of the available arguments:

Argument: -i

Description: Path to the input CSV file. The CSV file should contain two columns, where the first column contains the UniprotID of the pathogen protein, and the second column contains the UniprotID of the host protein.

Argument: -f

Description: Path to the input FASTA file. The FASTA file should contain sequences of all proteins listed in the provided list.

Argument: -o

Description: Path to the output directory. The results will be saved in this directory.

Argument: -b

Description: Specifies that the pathogen type is bacteria.

Example usage:

                    
                        python View.py -b -i input.csv -f input.fasta -o output_directory
                    
                

Argument: -v

Description: Specifies that the pathogen type is a virus, but it is unclear which family or species this pathogen originates from.

Example usage:

                    
                        python View.py -v -i input.csv -f input.fasta -o output_directory
                    
                

Argument: --vf

Description: Specifies that the pathogen is a virus, and we know it belongs to a specific family. Please provide the scientific family of the pathogen. The script only provides predictions for viruses within specific taxonomic families.

Example usage:

                    
                        python View.py --vf Corona -i input.csv -f input.fasta -o output_directory
                    
                

Other available abbreviations for virus families are as follows:

• Coronaviridae: Corona
• Filoviridae: Filo
• Flaviviridae: Flavi
• Hepeviridae: Hepe
• Herpesviridae: Herpes
• Orthomyxoviridae: Orthomyxo
• Paramyxoviridae: Paramyxo
• Parvoviridae: Parvo
• Retroviridae: Retro

If you want to predict for a virus family that is not listed here, please use the -v argument instead.

Argument: --vs

Description: Specifies that the pathogen is a virus, and we know it belongs to a specific species. Please provide the scientific species of the pathogen. The script only provides predictions for viruses within specific taxonomic species.

Example usage:

                    
                        python View.py --vs DENV -i input.csv -f input.fasta -o output_directory
                    
                

Other available abbreviations for virus species are as follows:

• DENV virus: DENV
• HCV virus: HCV
• HHV4 virus: HHV4
• HHV8 virus: HHV8
• HIV1 virus: HIV1
• InfluenzaA virus: InfluenzaA

If you want to predict for a virus species that is not listed here, please use the --vf or -v arguments instead.

Argument: -h

Description: Prints the help information.