Options

It is possible to customize the functions of PathwayMatcher using command line arguments.

Command line arguments

Argument	Description	Required
-t,--type <type>	The type of input: uniprot, rsid, peptide...	Yes
-i,--input <file>	Input file path and name relative to the location of the jar file.	Yes
-o,--output <file>	Output file path and name	No
-r,--range <int>	Plus minus positions for the same PTM site	No
-tlp, --toplevelpathways	Show the top level pathway column in result	No
-m, --matchType <type>	Proteoform match criteria	No
-g, --graph	Create default connection graph	No
-gg, --graphGene	Create gene connection graph	No
-gu, --graphProtein	Create protein connection graph	No
-gp, --graphProteoform	Create proteoform connection graph	No
-f, --fasta	Fasta file with proteins where to find the peptides	No
-h, --help	Print usage and available arguments	No
-v, --version	Print version of PathwayMatcher	No

• The paths to the files can be relative or absolute:

--input ./resources/.input.txt
--input C:/Users/User/WorkingFolder/resources/input.txt

Java configuration

In order to execute bigger queries in PathwayMatcher, it is recommended to use the following flags when executing the jar file.

Argument	Description
-d64	use a 64-bit data model if available
-Xmx<size>	set maximum Java heap size

For example:

java -d64 -Xmx10g -jar PathwayMatcher-1.2.jar -t uniprot -i data/uniprotList.txt -o data/output.csv

This will make sure that you use the 64-bit data model instead of the 32-bit model if possible. And will set the maximum Java heap size memory to 10 GB so that the program does not run out of memory during the execution.

Default values

If the configuration arguments for the PathwayMatcher are not specified in the command line, then they will take the default values.

Argument	Value
-r,--range	0
-tlp,--showTopLevelPathways	False
-m,--matchType	SUPERSET