Chris Mungall > go-perl-0.14 > go2fmt.pl

Download:
go-perl-0.14.tar.gz

Annotate this POD

CPAN RT

New  10
Open  1
View/Report Bugs
Source   Latest Release: go-perl-0.15

NAME ^

go2fmt.pl go2obo_xml go2owl go2rdf_xml go2obo_text

SYNOPSIS ^

  go2fmt.pl -w obo_xml -e errlog.xml ontology/*.ontology
  go2fmt.pl -w obo_xml -e errlog.xml ontology/gene_ontology.obo

DESCRIPTION ^

parses any GO/OBO style ontology file and writes out as a different format

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

-w|writer FORMAT

format for output - see below for list

-|xslt XSLT

The name or filename of an XSLT transform

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

  go2fmt.pl -xslt oboxml_to_owl go.obo

If the name is specified, then first of all $GO_ROOT/xml/xsl/*.xsl will be searched; if GO_ROOT is not set, then the perl modules dir where GO is installed will be searched (the xslts will be installed here automatically if you follow the normal install process)

-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.

This will bring a speed improvement for b<some> 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

FORMATS

writable formats are

go_ont

Files with suffix ".ontology"

These store the ontology DAGs

go_def

Files with suffix ".defs"

go_xref

External database references for GO terms

Files with suffix "2go" (eg ec2go, metacyc2go)

go_assoc

Annotations of genes or gene products using GO

Files with prefix "gene-association."

obo_text

Files with suffix ".obo"

This is a new file format replacement for the existing GO flat file formats. It handles ontologies, definitions and xrefs (but not associations)

obo_xml

Files with suffix ".obo.xml" or ".obo-xml"

This is the XML version of the OBO flat file format above

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

tbl

simple (lossy) tabular representation

summary

can be used on both ontology files and association files

pathlist

shows all paths to the root

owl

OWL format (default: OWL-DL)

OWL is a W3C standard format for ontologies

You will need the XSL files from the full go-dev distribution to run this; see the XML section in http://www.godatabase.org/dev

obj_yaml

a YAML representation of a GO::Model::Graph object

obj_storable

A dump of the perl GO::Model::Graph object. You need Storable from CPAN for this to work. This is intended to cache objects on the filesystem, for fast access. The obj_storable representation may not be portable

text_html

A html-ified OBO output format

godb_prestore

XML that maps directly to the GODB relational schema (can then be loaded using stag-storenode.pl)

chadodb_prestore

XML that maps directly to the Chado relational schema (can then be loaded using stag-storenode.pl)

DOCUMENTATION

http://www.godatabase.org/dev

syntax highlighting: