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This section identifies the command line arguments for BELC.

General Arguments

The following arguments are passed to the BELC compiler. Commonly used arguments have both a short and a long form.

Argument

Description

-h --help

Shows command line options.

-f [filename] --file

File name of an XBEL or BEL Script file to compile.

-p [path] --path

Path to a folder containing one or more XBEL or BEL Script files to compile.

-k [kam] --kam-name

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.

-d [description] --kam-description

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.

-s [filename] --system-config-file

Allows the user to specify the path to an alternative system configuration file to use to specify the BEL Framework configuration to use.
The default is to use the default systems configuration file found in [installdir]/config.

--debug

Enables debug mode for the compiler/assembler. Debug mode preserves intermediate files and exports an XGMML version of the KAM for debugging purposes.
The default is to disable debugging.

-v --verbose

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.
The default is to disable verbose mode.

-t --timing

Enables timing mode. This mode outputs times in seconds for each reported phase of the compiler/assemble. Usually used in conjunction with --verbose.
The default is to disable timing mode.

--pedantic

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.
The default is to disable pedantic mode.

--no-preserve

If present, if a KAM with the same name exists it will be overwritten.
The default is to overwrite the KAM.

Phase I Specific Arguments

These optional arguments are used to control the compilation of proto-networks during Phase I.

Argument

Description

--no-nested-statements

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.
The default is to couple nested statements.

--no-semantic-check

Bypasses the semantic checker. When set, this option will omit checking for semantic errors in the input documents.
The default is to enable semantic checking.

--no-syntax-check

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.
The default is to enable syntax checking.

Phase III Specific Arguments

These optional arguments are used to control the augmentation of the composite network during Phase III.

Argument

Description

--no-phaseIII

Executes Phase III in pass-through mode. This is the same as specifying --no-gene-scaffolding, --no-named-complexes and --no-protein-families.

--no-gene-scaffolding

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.
The default is to expand gene activation pathways for identified gene products.

--no-named-complexes

Modifies Phase III to omit coupling named complex members to existing nodes in the composite network.
The default is to automatically create edges from named complexes in a BEL Document to their components.

--no-protein-families

Modifies Phase III to omit coupling protein family members to existing nodes into the composite network.
The default is to automatically create edges from protein family nodes in a BEL Document to their members.

--no-orthology

Modifies Phase II to omit coupling of orthologous nodes to existing nodes in the composite network.
The default is to automatically create edges from geneAbundance, protein family, and named protein complex nodes in a BEL Document to the orthologous nodes from other species.

--expand-named-complexes

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.
The default is not to inject named complex nodes and edges.

--expand-protein-families

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.
The default is not to inject protein family nodes and edges.

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