Options - PathwayAnalysisPlatform/PathwayMatcher GitHub Wiki

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 <output_prefix> Path and prefix for the output files: search.tsv (list of reactions and pathways containing the input), analysis.tsv (over-representation analysis) and networks files. No
-T, --toplevelpathways Show the top level pathway column in result 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

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 <output_prefix> Path and prefix for the output files: search.tsv (list of reactions and pathways containing the input), analysis.tsv (over-representation analysis) and networks files. No
-T, --toplevelpathways Show the top level pathway column in result No
-r,--range <int> Integer number margin error for sites of PTMs. Only for modified peptides. No
-m, --matchType <type> Proteoform match criteria. Only modified peptides. 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

Command line arguments for proteoforms

Argument Description Required
-i,--input <file> Input file path and name relative to the location of the jar file. Yes
-m, --matchType <type> Proteoform match criteria No
-o,--output <output_prefix> Path and prefix for the output files No
-r,--range <int> Plus minus positions for the same PTM site No
-T, --toplevelpathways Show the top level pathway column in result 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
  • 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 SUBSET
-i, --input no value
-o, --output Empty string
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