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.\"
.IX Title "GO-DAG-SUMMARY 1"
.TH GO-DAG-SUMMARY 1 "2005-05-24" "perl v5.8.6" "User Contributed Perl Documentation"
.SH "NAME"
go\-dag\-summary
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  go-dag-summary ontology/gene_ontology.obo
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Summarises an ontology
.SH "ARGUMENTS"
.IX Header "ARGUMENTS"
\fI\-e \s-1ERRFILE\s0\fR
.IX Subsection "-e ERRFILE"
.PP
writes parse errors in \s-1XML\s0 \- defaults to \s-1STDERR\s0
(there should be no parse errors in well formed files)
.PP
\fI\-p \s-1FORMAT\s0\fR
.IX Subsection "-p FORMAT"
.PP
determines which parser to use; if left unspecified, will make a guess
based on file suffix. See below for formats
.Sh "\-use_cache"
.IX Subsection "-use_cache"
If this switch is specified, then caching mode is turned on.
.PP
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 \*(L".cache\*(R" suffix.
.PP
The next time you parse the file, this program will automatically
check for the existence of the \*(L".cache\*(R" 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.
.SH "OUTPUT"
.IX Header "OUTPUT"
One row per ontology
.PP
Each row has the following columns
.IP "input filename" 4
.IX Item "input filename"
.PD 0
.IP "total no of terms" 4
.IX Item "total no of terms"
.IP "total no of relationships" 4
.IX Item "total no of relationships"
.IP "total no of paths" 4
.IX Item "total no of paths"
.IP "avg no of paths per term (p/t)" 4
.IX Item "avg no of paths per term (p/t)"
.IP "maximum no of paths for any term" 4
.IX Item "maximum no of paths for any term"
.IP "\s-1ID\s0 of term with maximum no of paths" 4
.IX Item "ID of term with maximum no of paths"
.PD
\&\s-1NOTE:\s0 obsolete terms are not included
.Sh "\s-1DOCUMENTATION\s0"
.IX Subsection "DOCUMENTATION"
<http://www.godatabase.org/dev>
.Sh "\s-1SEE\s0 \s-1ALSO\s0"
.IX Subsection "SEE ALSO"
<http://www.fruitfly.org/~cjm/obol/doc/go\-complexity.html>
