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.\" ========================================================================
.\"
.IX Title "Bio::OntologyIO::goflat 3pm"
.TH Bio::OntologyIO::goflat 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::OntologyIO::goflat \- a parser for the Gene Ontology flat\-file format
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::OntologyIO;
\&
\&  # do not use directly \-\- use via Bio::OntologyIO
\&  my $parser = Bio::OntologyIO\->new
\&        ( \-format       => "go",
\&     \-defs_file    => "/home/czmasek/GO/GO.defs",
\&          \-files        => ["/home/czmasek/GO/component.ontology",
\&                            "/home/czmasek/GO/function.ontology",
\&                            "/home/czmasek/GO/process.ontology"] );
\&
\&  my $go_ontology = $parser\->next_ontology();
\&
\&  my $IS_A    = Bio::Ontology::RelationshipType\->get_instance( "IS_A" );
\&  my $PART_OF = Bio::Ontology::RelationshipType\->get_instance( "PART_OF" );
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Needs Graph.pm from \s-1CPAN.\s0
.PP
This is essentially a very thin derivation of the dagflat parser.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the 
Bioperl mailing lists  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Christian M. Zmasek
.PP
Email: czmasek\-at\-burnham.org  or  cmzmasek@yahoo.com
.PP
\&\s-1WWW:\s0   http://monochrome\-effect.net/
.PP
Address:
.PP
.Vb 3
\&  Genomics Institute of the Novartis Research Foundation
\&  10675 John Jay Hopkins Drive
\&  San Diego, CA 92121
.Ve
.SS "\s-1CONTRIBUTOR\s0"
.IX Subsection "CONTRIBUTOR"
.Vb 1
\& Hilmar Lapp, hlapp at gmx.net
.Ve
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 10
\& Title   : new
\& Usage   : $parser = Bio::OntologyIO\->new(
\&                             \-format => "go",
\&                             \-defs_file => "/path/to/GO.defs",
\&                             \-files => ["/path/to/component.ontology",
\&                                        "/path/to/function.ontology",
\&                                        "/path/to/process.ontology"] );
\& Function: Creates a new goflat parser.
\& Returns : A new goflat parser object, implementing Bio::OntologyIO.
\& Args    : \-defs_file  => the name of the file holding the term
\&                          definitions
\&           \-files      => a single ontology flat file holding the
\&                          term relationships, or an array ref holding
\&                          the file names (for GO, there will usually be
\&                          3 files: component.ontology, function.ontology,
\&                          process.ontology)
\&           \-file       => if there is only a single flat file, it may
\&                          also be specified via the \-file parameter
\&           \-ontology_name => the name of the ontology; if not specified the
\&                          parser will auto\-discover it by using the term
\&                          that starts with a $, and converting underscores
\&                          to spaces
\&           \-engine     => the Bio::Ontology::OntologyEngineI object
\&                          to be reused (will be created otherwise); note
\&                          that every Bio::Ontology::OntologyI will
\&                          qualify as well since that one inherits from the
\&                          former.
.Ve
.PP
See Bio::OntologyIO.