Scripts to create RegINs (Regulatory Interaction Networks) from tab files.
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This program allows you to create a RegIN file that can be used with CyTargetLinker from a tab-delimited file containing attributes for the source and target node as well as attributes for the edges.
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How to run the script with your own tab-delimited text file?
- Download the latest release from https://github.com/mkutmon/regin-creator/blob/master/releases/. You will need the jar file and the dependencies zip file which contains a lib directory with all dependencies. Unzip the dependencies.zip and make sure the lib directory is in the same directory as the jar file, so it can find all dependencies.
- Create a config file like the template here: https://github.com/mkutmon/regin-creator/blob/master/template.config.
- name = database name (required)
- organism = species (optional)
- version = database version (optional)
- source_columns = list of column numbers (starting with 0!) that are associated with the source nodes (separated with ",")
- target_columns = list of column numbers (starting with 0!) that are associated with the target nodes (separated with ",")
- edge_columns = list of column numbers (starting with 0!) that are associated with the edges (separated with ",")
- interaction_type = which kind of interaction does the file contain
- source_id_column = column that contains the identifier for source nodes (required)
- source_type = (gene, transcriptionFactor, drug, miRNA -> predefined) but you can also use others (required)
- source_bridgedb = path to the bridgedb file that should be used for the source nodes (optional)
- source_syscode_in = bridgedb system code for the source node identifiers (optional but required if bridgedb is used)
- source_syscode_out = list of bridgedb system codes that should be supported (optional but required if bridgedb is used) (separated with ",")
- source_label_column = column number (starting with 0!) which contains the nodel label for source nodes (required)
- target_id_column = column that contains the identifier for target nodes (required)
- target_type = (gene, transcriptionFactor, drug, miRNA -> predefined) but you can also use others (required)
- target_bridgedb = path to the bridgedb file that should be used for the target nodes (optional)
- target_syscode_in = bridgedb system code for the target node identifiers (optional but required if bridgedb is used)
- target_syscode_out = list of bridgedb system codes that should be supported (optional but required if bridgedb is used) (separated with ",")
- target_label_column = column number (starting with 0!) which contains the nodel label for target nodes (required)
- Run the converter file with the input file (tab delimited text file containing the interaction data), the config file (as described in point 2) and an output file (e.g. output.xgmml).
- java -jar -Dfile.encoding=UTF-8 converter-x.x.jar -i input.txt -o output.xgmml -c file.config