Author: Charles Plessy 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