GO-SHOW-PATHS-TO-ROOT(1p) User Contributed Perl Documentation GO-SHOW-PATHS-TO-ROOT(1p)NAME
go-show-paths-to-root.pl - shows all possible paths from a term to the top
SYNOPSIS
go-show-paths-to-root.pl -id GO:0008021 ontology/gene_ontology.obo
go-show-paths-to-root.pl -names -id GO:0008021 ontology/gene_ontology.obo
DESCRIPTION
traverses DAG showing all paths (terms and intervening relationships) to the root
This script is purely file based; it needs to parse the ontology each time
Subsequent parses can be speeded up using the use_cache option
If you wish to use the GO MySQL db, see the script go-db-show-paths-to-root.pl in the go-db-perl distribution
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.
DOCUMENTATION
<http://www.godatabase.org/dev>
perl v5.14.2 2010-05-12 GO-SHOW-PATHS-TO-ROOT(1p)
Check Out this Related Man Page
GO-DAG-SUMMARY(1p) User Contributed Perl Documentation GO-DAG-SUMMARY(1p)NAME
go-dag-summary - summarises an ontology
SYNOPSIS
go-dag-summary ontology/gene_ontology.obo
DESCRIPTION
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
DOCUMENTATION
<http://www.godatabase.org/dev>
SEE ALSO
http://www.fruitfly.org/~cjm/obol/doc/go-complexity.html <http://www.fruitfly.org/~cjm/obol/doc/go-complexity.html>
perl v5.14.2 2013-02-07 GO-DAG-SUMMARY(1p)
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