Options

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

PathwayMatcher has the following subcommands

Argument	Description
match-proteoforms	Match a list of proteoforms to reactions and pathways
match-genes	Match a list of gene names
match-uniprot	Match a list of UniProt protein accessions
match-ensembl	Match a list of Ensembl protein identifiers
match-vcf	Match a list of genetic variants in VCF format
match-chrbp	Match a list of genetic variants as chromosome and base pairs
match-rsids	Match a list of genetic variants as RsIds
match-peptides	Match a list of peptides
match-modified-peptides	Match a list of peptides with post translational modifications
help	Displays help information about the specified command

Command line arguments for genes, uniprot, ensembl, vcf, chrbp and rsids

Argument	Description	Required
-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
-T, --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, --graphUniprot	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

Command line arguments for peptides and modified peptides

Argument	Description	Required
-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
-T, --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, --graphUniprot	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

Command line arguments for proteoforms

Argument	Description	Required
-g, --graph	Create default connection graph	No
-gg, --graphGene	Create gene connection graph	No
-gu, --graphUniprot	Create protein connection graph	No
-gp, --graphProteoform	Create proteoform connection graph	No
-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
-T, --toplevelpathways	Show the top level pathway column in result	No
-m, --matchType <type>	Proteoform match criteria	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

-g, --graph Create default connection graph according to input type. -gg, --graphGene Create gene connection graph -gp, --graphProteoform Create proteoform connection graph -gu, --graphUniprot Create protein connection graph -i, --input=<input_path> Input file with path -m, --matchType= Proteoform match criteria. Valid values: STRICT, SUPERSET, SUPERSET_NO_TYPES, SUBSET, SUBSET_NO_TYPES, ONE, ONE_NO_TYPES. Default: SUBSET -o, --output=<output_path> Path to directory for the output files: search.tsv (list of reactions and pathways containing the input), analysis.tsv (over-representation analysis) and networks files. -r, --range= Integer range of error for PTM sites. Default: 0 -T, --topLevelPathways Show Top Level Pathways in the search result.

• 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 match-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
-T,--showTopLevelPathways	False
-m,--matchType	SUPERSET