.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.43) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "GO-DAG-SUMMARY 1p" .TH GO-DAG-SUMMARY 1p "2023-12-18" "perl v5.36.0" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" go\-dag\-summary \- summarises an ontology .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 .SS "\-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 .SS "\s-1DOCUMENTATION\s0" .IX Subsection "DOCUMENTATION" .SS "\s-1SEE ALSO\s0" .IX Subsection "SEE ALSO"