go-filter-subset(1p) [debian man page]
GO-FILTER-SUBSET(1p) User Contributed Perl Documentation GO-FILTER-SUBSET(1p) NAME
go-filter-subset.pl - extracts a subgraph from an ontology file SYNOPSIS
go-filter-subset.pl -id GO:0003767 go.obo go-filter-subset.pl -id GO:0003767 -to png go.obo | xv - go-filter-subset.pl -filter_code 'sub{shift->name =~ /transcr/}' go.obo DESCRIPTION
Exports a subset of an ontology from a file. The subset can be based on a specified set of IDs, a preset "subset" filter in the ontology file (eg a GO "slim" or subset), or a user-defined filter. The subset can be exported in any format, including a graphical image ARGUMENTS
-id ID ID to use as leaf node in subgraph. All ancestors of this ID are included in the exported graph (unless -partial is set) Multiple IDs can be passed -id ID1 -id ID2 -id ID3 ....etc -subset SUBSET_ID Extracts a named subset from the ontology file. (only works with obo format files). For example, a specific GO slim ONLY terms belonging to the subset are exported - the -partial option is automatically set -namespace NAMESPACE only terms in this namespace -filter_code SUBROUTINE advanced option A subroutine with which the GO::Model::Term object is tested for inclusion in the subgraph (all ancestors are automatically included) You should have an understanding of the go-perl object model before using this option Example: go-filter-subset -filter_code 'sub {shift->namespace eq 'molecular_function'}' go.obo (the same things can be achieved with the -namespace option) -partial If this is set, then only terms that match the user query are included. Parentage is set to the next recursive parent node in the filter For example, with the -subset option: if X and Y belong to the subset, and Z does not, and X is_a Z is_a Y, then the exported graph withh have X is_a Y -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. DOCUMENTATION <http://www.godatabase.org/dev> perl v5.14.2 2010-05-12 GO-FILTER-SUBSET(1p)
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go-perl(3pm) User Contributed Perl Documentation go-perl(3pm) NAME
go-perl - perl modules for GO and other OBO ontologies SYNOPSIS
# ** FETCHING GRAPH OBJECTS FROM AN ONTOLOGY FILE ** use GO::Parser; my $parser = new GO::Parser({handler=>'obj'}); # create parser object $parser->parse("gene_ontology.obo"); # parse file -> objects my $graph = $parser->handler->graph; # get L<GO::Model::Graph> object my $term = $graph->get_term("GO:0001303"); # fetch a term by ID printf "Got term: %s %s ", $term->acc, $term->name; my $ancestor_terms = $graph->get_recursive_parent_terms($term->acc); foreach my $anc_term (@$ancestor_terms) { printf " Ancestor term: %s %s ", $anc_term->acc, $anc_term->name; } # ** FROM THE COMMAND LINE ** (requires go-dev/xml) go2xml gene_ontology.obo | xsltproc $GO_ROOT/xml/xsl/my-transform.xsl - DESCRIPTION
go-perl is part of the go-dev code distribution. It is also available as a seperate library in its own right. go-perl is a collection of perl modules for working with ontologies and data, in particular the Gene Ontology and other Open Bio- Ontologies. For background on these projects, see http://www.geneontology.org http://obo.sourceforge.net go-perl provides the following functionality: parsers Biological ontologies and associated data come in assorted formats. See: GO::Parser handlers/writers All parsers are XML event based - they emit Obo-XML, which can be caught by different handlers. Some of these handlers effectively transform the parsed file into a different format or summary. If you are not interested in generating XML, you can use an object handler, which will give you objects for traversing an ontology; see below a graph-based object model Biological ontologies typically have graph-based structures (DAGs). go-perl provides a perl object model representing ontologies and associations to ontologies. Classes include: GO::Model::Term -- a node/term within an ontology GO::Model::Graph -- collection of terms and the relationships between them GO::Model::Relationship -- a typed relationship between two terms GO::Model::Xref -- a database xref, for a term or any other object GO::Model::Association -- an association between a term and a gene product GO::Model::GeneProduct -- a gene or product of a gene or similar annotated entity GO::Model::Evidence -- supporting evidence for an association GO::Model::Seq -- a biological sequence of residues for a gene product SIMPLE PROGRAMMERS INTERFACE GO::Basic simple procedural access to GO files SCRIPTS
These scripts come as part of the go-perl distribution map2slim Given a GO slim file, and a current ontology (in one or more files), this script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. The script can be used to either create a new gene association file, containing the most pertinent GO slim accessions, or in count-mode, in which case it will give distinct gene product counts for each slim term. for full instructions, see map2slim go-dag-summary.pl Generates a summary of the DAG structure of an ontology file A row will be generated for every ontology in the file, with the following data 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 for full instructions, see go-dag-summary.pl go-show-paths-to-root.pl Will show all possible paths from a term to the root/top in the ontology for full instructions, see go-show-paths-to-root.pl go-apply-xslt Will apply a GO XSL transform (by name) on an OBO-XML file For a full list of XSLs available, see <http://www.godatabase.org/xml/xsl> go-export-graph.pl Writes an obo file out as an ascii-tree, a graphviz PNG or other format for full instructions, see go-export-graph.pl go-show-assocs-by-node.pl given a GO ontology file and an association file and a term ID, will list all products associated to that ID for full instructions, see go-show-assocs-by-node.pl go-filter-subset.pl Exports a subset of an ontology from a file. The subset can be based on a specified set of IDs, a preset "subset" filter in the ontology file (eg a GO "slim" or subset), or a user-defined filter. The subset can be exported in any format, including a graphical image for full instructions, see go-filter-subset.pl go2fmt.pl generic file converter. This will convert any go/obo formatted file such as ontology files and association files and write output in some other format or report. See the full list of convenience scripts below. for full instructions, see go2fmt.pl go2chadoxml converts a file in any valid go/obo format to chadoxml. See also go2fmt.pl go2godb_prestore converts a file in any valid go/obo format to an xml format that is isomorphic to the GO MySQL Db schema, and can be loaded with DBIx::DBStag. See also go2fmt.pl go2error_report converts a file in any valid go/obo format to error_report. See also go2fmt.pl go2obo_test (alias: go2obo) converts a file in any valid go/obo format to obo. See also go2fmt.pl go2obo_html converts a file in any valid go/obo format to obo_html. See also go2fmt.pl go2obo_xml (alias: go2xml) converts a file in any valid go/obo format to obo_xml. See also go2fmt.pl go2owl converts a file in any valid go/obo format to owl. See also go2fmt.pl go2pathlist converts a file in any valid go/obo format to pathlist. See also go2fmt.pl go2prolog converts a file in any valid go/obo format to prolog. See also go2fmt.pl go2rdfxml converts a file in any valid go/obo format to rdfxml. See also go2fmt.pl go2summary converts a file in any valid go/obo format to summary. See also go2fmt.pl go2sxpr converts a file in any valid go/obo format to sxpr. See also go2fmt.pl go2tbl converts a file in any valid go/obo format to tbl. See also go2fmt.pl go2text_html converts a file in any valid go/obo format to text_html. See also go2fmt.pl RELATED PACKAGES
Download the full go-dev distribution for access to more functionality. go-perl is a subset of go-dev go-dev includes the following: go-perl This package http://www.godatabase.org/dev/go-perl/doc/go-perl-doc.html go-db-perl Database API for use in conjunction with go-perl Allows for loading of GO databases and fetching graph objects from the database http://www.godatabase.org/dev/go-db-perl/doc/go-db-perl-doc.html GO::AppHandle amigo Ontology browser, written in perl Requires installation of both go-perl and go-db-perl java The DAG-Edit curation tool http://www.godatabase.org/dev xml DTDs for the Obo-XML format, and XSL stylesheets for converting to and from Obo-XML format http://www.godatabase.org/dev/xml/doc/xml-doc.html sql Schema and SQL code for the GO database http://www.godatabase.org/dev/sql/doc/godb-sql-doc.html AUTHORS
(C) Chris Mungall 2000-2006 This module is free software. You may distribute under the same terms as perl itself. perl v5.14.2 2010-08-10 go-perl(3pm)