NAME

go-dag-summary

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