This section identifies the command line arguments for BELC.
The following arguments are passed to the BELC compiler. Commonly used arguments have both a short and a long form.
Shows command line options.
File name of an XBEL or BEL Script file to compile.
Path to a folder containing one or more XBEL or BEL Script files to compile.
Name of the KAM to create. If a KAM with the same name exists it will be overwritten if the --no-preserve option is set.
A description for the KAM that will be created. Put the description in quotes. It may be necessary to escape the quotes (i.e. \") for the full description to be recognized by BELC.
Allows the user to specify the path to an alternative system configuration file to use to specify the BEL Framework configuration to use.
Enables debug mode for the compiler/assembler. Debug mode preserves intermediate files and exports an XGMML version of the KAM for debugging purposes.
Enables verbose mode. This mode outputs information about the different stages of each compiler/assembler phase. Usually used in conjunction with --timing to gather information about the compilation process.
Enables timing mode. This mode outputs times in seconds for each reported phase of the compiler/assemble. Usually used in conjunction with --verbose.
Enables pedantic mode. This mode treats warnings as errors and will terminate the compiler/assembler at the end of a phase if a warning is generated in the phase.
If present, if a KAM with the same name exists it will be overwritten.
Phase I Specific Arguments
These optional arguments are used to control the compilation of proto-networks during Phase I.
Modifies Phase I to force the compiler not to create a relationship between the subject term of a statement with a nested statement as the object, to the object term of the nested statement.
Bypasses the semantic checker. When set, this option will omit checking for semantic errors in the input documents.
Bypasses the syntax checker. When set, this option will omit checking for syntax errors in the input documents. This is not recommended as it can lead to unpredictable KAM topologies.
Phase III Specific Arguments
These optional arguments are used to control the augmentation of the composite network during Phase III.
Executes Phase III in pass-through mode. This is the same as specifying --no-gene-scaffolding, --no-named-complexes and --no-protein-families.
Modifies Phase III to omit expanding the composite network to include gene activation pathways for gene products identified in a BEL Document input to the compiler.
Modifies Phase III to omit coupling named complex members to existing nodes in the composite network.
Modifies Phase III to omit coupling protein family members to existing nodes into the composite network.
Modifies Phase II to omit coupling of orthologous nodes to existing nodes in the composite network.
Modifies Phase III to inject named complex components and associated hasComponent edges when a component of a named complex is defined in a BEL Document.
Modifies Phase III to inject protein family nodes, members and associated hasMember edges when a member of a protein family is defined in a BEL Document.