NAME
go-dag-summary
SYNOPSIS
go-dag-summary ontology/gene_ontology.oboDESCRIPTION
Summarises an ontology
ARGUMENTS
-e ERRFILE
writes parse errors in XML - defaults to STDERR (there should be no parse errors in well formed files)
-p FORMAT
determines which parser to use; if left unspecified, will make a guess based on file suffix. See below for formats
-use_cache
If this switch is specified, then caching mode is turned on.
With caching mode, the first time you parse a file, then an additional file will be exported in a special format that is fast to parse. This file will have the same filename as the original file, except it will have the ".cache" suffix.
The next time you parse the file, this program will automatically check for the existence of the ".cache" file. If it exists, and is more recent than the file you specified, this is parsed instead. If it does not exist, it is rebuilt.
OUTPUT
One row per ontology
Each row has the following columns
- input filename
- total no of terms
- total no of relationships
- total no of paths
- avg no of paths per term (p/t)
- maximum no of paths for any term
- ID of term with maximum no of paths
-
NOTE: obsolete terms are not included