svr_project_model

Project atomic regulons from model to new genome.

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Example:

    svr_project_model -a AtomicRegulons -e Effectors -g TargetGenome -m ModelDir

would produce a directory called "MOdelDir" that contained

    atomic.regulons  [ a file defining the projeted atomic.regulons ]
    effectors        [ a file of predicted effectors ]
    errors           [ a log of problems encountered in the projection ]
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Command-Line Options

-a AtomicRegulons

This is used to specify a set of atomic regulons that are to be projected. The first two columns of the table must contain

    [atomic.reg.id,PEG-id]

-e Effectors

This is used to suggest effectors of expression. The first column must contain an atomic regulon number. The second to last column must contain a code indicting the type of regulation (-,+,+-, or u). The last column contains the effector. Each line may be thought of as stating that the effector activates or represses expression of the atomic regulon.

-g TargetGenome

This specifies the genome to which the projection is made

-m ModelDir

The program creates a directory (ModelDir) that will contain

    atomic.regulons - a projection of the atomic regulons expressed
                      as a 2 column table [Id,Gene-in-atomic-regulon]

    effectors       - a projection of the effetors expressed as 3 columns
                        [atomic-regulon,impact-of-effector,effector]

Output

The output is the ModelDir containing two files, one specifying the atomic regulons, and one the effectors. We allow singleton atomic regulons. They should be thought of as a means of reflecting the impact of an effector on a single gene (although some singletons have no associated effectors).