Documentation read from 04/17/2019 22:07:26 version of /vol/public-pseed/FIGdisk/FIG/bin/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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This is a path to the old SEED directory from which assignments and annotations are inherited
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