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|
Author: Charles Plessy <plessy@debian.org>
Forwarded: http://rt.cpan.org/Public/Bug/Display.html?id=37324
Description: Gives a whatis entry to each manpages
A manual page should start with a `NAME' section, which lists the name and a
brief description of the page separated by '\-'. These sections are parsed by
`mandb' and stored in a database for the use of `apropos' and `whatis'.
--- a/GO/Handlers/base.pm
+++ b/GO/Handlers/base.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::base -
+ GO::Handlers::base - default handler
=head1 SYNOPSIS
--- a/GO/Handlers/go_def.pm
+++ b/GO/Handlers/go_def.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::go_def -
+ GO::Handlers::go_def - go_def handler
=head1 SYNOPSIS
--- a/GO/Handlers/go_ont.pm
+++ b/GO/Handlers/go_ont.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::go_ont -
+ GO::Handlers::go_ont - go_ont handler
=head1 SYNOPSIS
--- a/GO/Handlers/go_xref.pm
+++ b/GO/Handlers/go_xref.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::go_xref -
+ GO::Handlers::go_xref - go_xref handler
=head1 SYNOPSIS
--- a/GO/Handlers/godb_prestore.pm
+++ b/GO/Handlers/godb_prestore.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::godb_prestore - transforms OBO XML to GODB XML
+ GO::Handlers::godb_prestore - transforms OBO XML to GODB XML
=head1 SYNOPSIS
--- a/GO/Handlers/obo_godb_flat.pm
+++ b/GO/Handlers/obo_godb_flat.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::obo_godb_flat -
+ GO::Handlers::obo_godb_flat - transforms OBO XML to MySQL tables
=head1 SYNOPSIS
--- a/GO/Handlers/obo_html.pm
+++ b/GO/Handlers/obo_html.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::obo_html -
+ GO::Handlers::obo_html - OBO HTML handler
=head1 SYNOPSIS
--- a/GO/Handlers/obo_text.pm
+++ b/GO/Handlers/obo_text.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::obo_text -
+ GO::Handlers::obo_text - OBO text handler
=head1 SYNOPSIS
--- a/GO/Handlers/owl_to_obo_text.pm
+++ b/GO/Handlers/owl_to_obo_text.pm
@@ -7,7 +7,7 @@
=head1 NAME
-Bio::Parser::owl_to_obo_text
+Bio::Parser::owl_to_obo_text - private module
=head1 SYNOPSIS
--- a/GO/Handlers/summary.pm
+++ b/GO/Handlers/summary.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::summary -
+ GO::Handlers::summary - summary about handlers
=head1 SYNOPSIS
--- a/GO/Handlers/tbl.pm
+++ b/GO/Handlers/tbl.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::tbl -
+ GO::Handlers::tbl - TBL handler
=head1 SYNOPSIS
--- a/GO/Handlers/text_html.pm
+++ b/GO/Handlers/text_html.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::text_html -
+ GO::Handlers::text_html - Text HTML handler
=head1 SYNOPSIS
--- a/GO/Handlers/xsl_base.pm
+++ b/GO/Handlers/xsl_base.pm
@@ -9,7 +9,7 @@
=head1 NAME
- GO::Handlers::text_html -
+ GO::Handlers::text_html - text HTML handler
=head1 SYNOPSIS
--- a/scripts/go-export-graph.pl
+++ b/scripts/go-export-graph.pl
@@ -43,7 +43,7 @@
=head1 NAME
-go-export-graph.pl
+go-export-graph.pl - exports a graph
=head1 SYNOPSIS
--- a/scripts/go2fmt.pl
+++ b/scripts/go2fmt.pl
@@ -97,11 +97,7 @@
=head1 NAME
-go2fmt.pl
-go2obo_xml
-go2owl
-go2rdf_xml
-go2obo_text
+go2fmt, go2obo_xml, go2owl, go2rdf_xml, go2obo_text - conversion tool and its wrappers
=head1 SYNOPSIS
--- a/GO/IO/Dotty.pm
+++ b/GO/IO/Dotty.pm
@@ -4,7 +4,7 @@
=head1 NAME
- GO::IO::Dotty;
+ GO::IO::Dotty - Dotty diagrams from GO graphs
=head1 SYNOPSIS
--- a/GO/IO/OBDXML.pm
+++ b/GO/IO/OBDXML.pm
@@ -18,7 +18,7 @@
=head1 NAME
- GO::IO::OBDXML;
+ GO::IO::OBDXML - dump GO terms as xml
=head1 SYNOPSIS
--- a/GO/IO/ObanOwl.pm
+++ b/GO/IO/ObanOwl.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::IO::ObanOwl;
+ GO::IO::ObanOwl - dump GO terms as xml
=head1 SYNOPSIS
--- a/GO/IO/RDFXML.pm
+++ b/GO/IO/RDFXML.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::IO::RDFXML;
+ GO::IO::RDFXML - dump GO terms as xml
=head1 SYNOPSIS
--- a/GO/IO/go_assoc.pm
+++ b/GO/IO/go_assoc.pm
@@ -15,7 +15,7 @@
=head1 NAME
- GO::IO::go_assoc;
+ GO::IO::go_assoc - dump GO terms as OBD XML
=head1 SYNOPSIS
--- a/GO/Model/Association.pm
+++ b/GO/Model/Association.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::Association;
+ GO::Model::Association - association between a GO term and a gene product
=head1 SYNOPSIS
--- a/GO/Model/CrossProduct.pm
+++ b/GO/Model/CrossProduct.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::CrossProduct;
+ GO::Model::CrossProduct - intersection between class/term and list of anonymous subclass
=head1 SYNOPSIS
--- a/GO/Model/DB.pm
+++ b/GO/Model/DB.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::DB;
+ GO::Model::DB - DB class
=head1 SYNOPSIS
--- a/GO/Model/Evidence.pm
+++ b/GO/Model/Evidence.pm
@@ -12,7 +12,7 @@
=head1 NAME
- GO::Model::Evidence;
+ GO::Model::Evidence - evidence for an association
=head1 SYNOPSIS
--- a/GO/Model/GeneProduct.pm
+++ b/GO/Model/GeneProduct.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::GeneProduct;
+ GO::Model::GeneProduct - gene product in a particular species
=head1 DESCRIPTION
--- a/GO/Model/GraphIterator.pm
+++ b/GO/Model/GraphIterator.pm
@@ -12,7 +12,7 @@
=head1 NAME
- GO::Model::GraphIterator;
+ GO::Model::GraphIterator - Graph iterator
=head1 SYNOPSIS
--- a/GO/Model/LogicalDefinition.pm
+++ b/GO/Model/LogicalDefinition.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::LogicalDefinition;
+ GO::Model::LogicalDefinition - logical definition
=head1 SYNOPSIS
--- a/GO/Model/Modification.pm
+++ b/GO/Model/Modification.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::Modification;
+ GO::Model::Modification - cross reference to external database
=head1 DESCRIPTION
--- a/GO/Model/Ontology.pm
+++ b/GO/Model/Ontology.pm
@@ -12,7 +12,7 @@
=head1 NAME
- GO::Model::Ontology;
+ GO::Model::Ontology - synonym for GO::Model::Graph
=head1 SYNOPSIS
--- a/GO/Model/Path.pm
+++ b/GO/Model/Path.pm
@@ -12,7 +12,7 @@
=head1 NAME
- GO::Model::Path;
+ GO::Model::Path - path between two nodes
=head1 SYNOPSIS
--- a/GO/Model/Property.pm
+++ b/GO/Model/Property.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::Property;
+ GO::Model::Property - model property
=head1 SYNOPSIS
--- a/GO/Model/Relationship.pm
+++ b/GO/Model/Relationship.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::Relationship
+ GO::Model::Relationship - relationship between two terms
=head1 SYNOPSIS
--- a/GO/Model/Restriction.pm
+++ b/GO/Model/Restriction.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::Restriction;
+ GO::Model::Restriction - model restriction
=head1 SYNOPSIS
--- a/GO/Model/Root.pm
+++ b/GO/Model/Root.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::Root
+ GO::Model::Root - base class for all GO::Model objects
=head1 DESCRIPTION
--- a/GO/Model/Seq.pm
+++ b/GO/Model/Seq.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::Seq;
+ GO::Model::Seq - biological sequence
=head1 SYNOPSIS
--- a/GO/Model/Species.pm
+++ b/GO/Model/Species.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::Species;
+ GO::Model::Species - gene product in a particular species
=head1 DESCRIPTION
--- a/GO/Model/Term.pm
+++ b/GO/Model/Term.pm
@@ -12,7 +12,7 @@
=head1 NAME
-GO::Model::Term - a term or concept in an ontology
+GO::Model::Term - a term or concept in an ontology
=head1 SYNOPSIS
--- a/GO/Model/TreeIterator.pm
+++ b/GO/Model/TreeIterator.pm
@@ -13,7 +13,7 @@
=head1 NAME
- GO::Model::GraphIterator;
+ GO::Model::GraphIterator - wraps GO::Model::GraphIterator
=head1 SYNOPSIS
--- a/GO/Model/Xref.pm
+++ b/GO/Model/Xref.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::Model::Xref;
+ GO::Model::Xref - cross reference to an external database
=head1 SYNOPSIS
--- a/GO/Parsers/locuslink_parser.pm
+++ b/GO/Parsers/locuslink_parser.pm
@@ -6,7 +6,7 @@
=head1 NAME
-GO::Parsers::locuslink_parser -
+GO::Parsers::locuslink_parser - Parser for LocusLink
=head1 SYNOPSIS
--- a/GO/Parsers/ncbi_taxonomy_parser.pm
+++ b/GO/Parsers/ncbi_taxonomy_parser.pm
@@ -10,7 +10,7 @@
=head1 NAME
- GO::Parsers::ncbi_taxonomy_parser
+ GO::Parsers::ncbi_taxonomy_parser - Parser for NCBI taxonomy
=head1 SYNOPSIS
--- a/GO/Parsers/obj_emitter.pm
+++ b/GO/Parsers/obj_emitter.pm
@@ -10,7 +10,7 @@
=head1 NAME
-GO::Parsers::obj_emitter -
+GO::Parsers::obj_emitter - Private class
=head1 SYNOPSIS
--- a/GO/ObjCache.pm
+++ b/GO/ObjCache.pm
@@ -11,7 +11,7 @@
=head1 NAME
- GO::ObjCache;
+ GO::ObjCache - private method
=head1 DESCRIPTION
--- a/GO/Utils.pm
+++ b/GO/Utils.pm
@@ -20,6 +20,10 @@
use Carp;
use Data::Dumper;
+=head1 NAME
+
+GO::Utils - utilities for GO modules
+
=head2 rearrange()
Usage : n/a
--- a/scripts/go-dag-summary.pl
+++ b/scripts/go-dag-summary.pl
@@ -110,7 +110,7 @@
=head1 NAME
-go-dag-summary
+go-dag-summary - summarises an ontology
=head1 SYNOPSIS
|
