.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40) .\" .\" 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 "GO2FMT 1p" .TH GO2FMT 1p "2021-01-09" "perl v5.32.0" "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" go2fmt, go2obo_xml, go2owl, go2rdf_xml, go2obo_text \- conversion tool and its wrappers .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 2 \& go2fmt.pl \-w obo_xml \-e errlog.xml ontology/*.ontology \& go2fmt.pl \-w obo_xml \-e errlog.xml ontology/gene_ontology.obo .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" parses any \s-1GO/OBO\s0 style ontology file and writes out as a different format .SS "\s-1ARGUMENTS\s0" .IX Subsection "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 .PP \fI\-w|writer \s-1FORMAT\s0\fR .IX Subsection "-w|writer FORMAT" .PP format for output \- see below for list .PP \fI\-|xslt \s-1XSLT\s0\fR .IX Subsection "-|xslt XSLT" .PP The name or filename of an \s-1XSLT\s0 transform .PP This can either be an absolute path to a file anywhere on the filesystem, or it can just be the name of the xslt; eg .PP .Vb 1 \& go2fmt.pl \-xslt oboxml_to_owl go.obo .Ve .PP If the name is specified, then first of all \f(CW$GO_ROOT\fR/xml/xsl/*.xsl will be searched; if \s-1GO_ROOT\s0 is not set, then the perl modules dir where \s-1GO\s0 is installed will be searched (the xslts will be installed here automatically if you follow the normal install process) .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. .PP This will bring a speed improvement for b of the output formats below (such as pathlist). Most output formats work with event-based parsing, so caching the object brings no benefit and will in fact be slower than bypassing the cache .SS "\s-1FORMATS\s0" .IX Subsection "FORMATS" writable formats are .IP "go_ont" 4 .IX Item "go_ont" Files with suffix \*(L".ontology\*(R" .Sp These store the ontology DAGs .IP "go_def" 4 .IX Item "go_def" Files with suffix \*(L".defs\*(R" .IP "go_xref" 4 .IX Item "go_xref" External database references for \s-1GO\s0 terms .Sp Files with suffix \*(L"2go\*(R" (eg ec2go, metacyc2go) .IP "go_assoc" 4 .IX Item "go_assoc" Annotations of genes or gene products using \s-1GO\s0 .Sp Files with prefix \*(L"gene-association.\*(R" .IP "obo_text" 4 .IX Item "obo_text" Files with suffix \*(L".obo\*(R" .Sp This is a new file format replacement for the existing \s-1GO\s0 flat file formats. It handles ontologies, definitions and xrefs (but not associations) .IP "obo_xml" 4 .IX Item "obo_xml" Files with suffix \*(L".obo.xml\*(R" or \*(L".obo\-xml\*(R" .Sp This is the \s-1XML\s0 version of the \s-1OBO\s0 flat file format above .IP "prolog" 4 .IX Item "prolog" prolog facts \- you will need a prolog compiler/interpreter to use these. You can reason over these facts using Obol or the forthcoming Bio-LP project .IP "tbl" 4 .IX Item "tbl" simple (lossy) tabular representation .IP "summary" 4 .IX Item "summary" can be used on both ontology files and association files .IP "pathlist" 4 .IX Item "pathlist" shows all paths to the root .IP "owl" 4 .IX Item "owl" \&\s-1OWL\s0 format (default: OWL-DL) .Sp \&\s-1OWL\s0 is a W3C standard format for ontologies .Sp You will need the \s-1XSL\s0 files from the full go-dev distribution to run this; see the \s-1XML\s0 section in .IP "obj_yaml" 4 .IX Item "obj_yaml" a \s-1YAML\s0 representation of a GO::Model::Graph object .IP "obj_storable" 4 .IX Item "obj_storable" A dump of the perl GO::Model::Graph object. You need Storable from \s-1CPAN\s0 for this to work. This is intended to cache objects on the filesystem, for fast access. The obj_storable representation may not be portable .IP "text_html" 4 .IX Item "text_html" A html-ified \s-1OBO\s0 output format .IP "godb_prestore" 4 .IX Item "godb_prestore" \&\s-1XML\s0 that maps directly to the \s-1GODB\s0 relational schema (can then be loaded using stag\-storenode.pl) .IP "chadodb_prestore" 4 .IX Item "chadodb_prestore" \&\s-1XML\s0 that maps directly to the Chado relational schema (can then be loaded using stag\-storenode.pl) .SS "\s-1DOCUMENTATION\s0" .IX Subsection "DOCUMENTATION"