Java How to run

The program runs in the command line or from a shell.

• Open a command prompt located in the folder that contains the "PathwayQuery-X.X.jar" file.
• Execute the following instruction in the command prompt:

java -jar PathwayQuery-X.X.jar [options]

Examples

Get graph for all proteins and all types of interactions. Use only command line arguments, no configuration file.

java -jar PathwayQuery-X.X.jar -l -c ../../config.txt

Get graph for all proteins and a some types of interactions. Provide configuration file.

java -jar PathwayQuery-X.X.jar -l -io -co -ro -c

Get graph for a custom list of proteins and some types of interactions. Use command line arguments.

java -jar PathwayQuery-X.X.jar -i resources/Input/customList.txt -o ./output.txt -l -io -co -ro

Get graph where all proteins are participants of reactions with the first reference publication before/at some year. Filter the interactions to be only: [input,catalyst,regulator] to output.

java -jar PathwayQuery-X.X.jar -y 1973 -io -co -ro

Get graph where the input set of proteins are participants of reactions with the first reference publication before/at some year.

java -jar PathwayQuery-X.X.jar -i <path>/customList.txt -y 1973