svr_inherit_annotations

Cause a new genome to inherit annotations from an existing genome for protein-encoding genes that are unique within each genome and that have identical translations.

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Example:

    svr_inherit_annotations OldSEEDdir NewSEEDdir User

would alter the contents of the NewSEEDdir. Each directory may contain a file called "rewrite.functions". These are 2-column tables [function,normalized.function]. We will speak of "corresponding genes". These are genes that can unambiguously be identified in each genome, and they have identical translations.

    1. The assigned functions will be calculated as follows:

       Let Gn be a gene in the new genome.  The rewrite.functions in the
       new directory will be a superset of the rewrite.functions in the old directory.

       Let Fn be the initial function of Gn (the value in the
       assigned_functions file).  If the rewrite.functions specifies a
       rewrite to Fn' for Fn, then Fn' is the value placed into the
       assigned_functions file (and an annotation indicating the change
       is recorded).  If there is no rewrite rule in the old
       rewrite.functions, and there is a corresponding gene in the old
       directory with function Fo and Fo is not Fn, then Fo is the
       value placed in the new assigned_functions, and

           a. Fn -> Fo becomes a rewrite in the new rewrite.functions,

           b. an annotation is added designating the change (at the current time).

       Otherwise, Fn is retained.

    2. The annotations in the new directory become a merge of the annotations
       in the old and new directories.

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Command-Line Options

oldSEEDdir

This is a path to the old SEED directory from which assignments and annotations are inherited

newSEEDdir

This is a path to the new SEED directory which inherits assignments and annotations.

-item User

This is the user credited with making the changes to the functions