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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Geneid 3pm"
.TH Bio::Tools::Geneid 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tools::Geneid \- Results of one geneid run
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  use Bio::Tools::Geneid;
\&  my $gid = Bio::Tools::Geneid(\-file => "geneid.out");
\&
\&  while (my $gene = $gid\->next_prediction)
\&  {
\&    my @transcripts = $gene\->transcripts;
\&      foreach my $t (@transcripts)
\&      {
\&        my @exons = $t\->exons;
\&        foreach my $e (@exons)
\&        {
\&          printf("Exon %d..%d\en", $e\->start, $e\->end);
\&        }
\&      }
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is the parser for the output of geneid by Enrique Blanco and
Roderic Guigó (IMIM-UPF). See http://www1.imim.es/software/geneid. It
relies on native geneid output format internally and will work with
geneid versions 1.0 and 1.1. Currently this module supports only the
default mode of operation which is to predict exons and assemble an
optimal gene prediction.
.PP
It takes either a file handle or a file name and returns a
Bio::SeqFeature::Gene::GeneStructure object.
.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 one
of 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 \- Keith James"
.IX Header "AUTHOR - Keith James"
.Vb 1
\& Email: kdj@sanger.ac.uk
.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 6
\& Title   : new
\& Usage   : $obj\->new(\-file = "<geneid.out");
\&           $obj\->new(\-fh => \e*GI);
\& Function: Constructor for geneid wrapper. Takes either a file
\&         : or filehandle
\& Returns : L<Bio::Tools::Geneid>
.Ve
.SS "next_prediction"
.IX Subsection "next_prediction"
.Vb 9
\& Title   : next_prediction
\& Usage   : while($gene = $geneid\->next_prediction)
\&           {
\&               # do something
\&           }
\& Function: Returns the gene structure prediction of the geneid result
\&           file. Call this method repeatedly until FALSE is returned.
\& Returns : A Bio::SeqFeature::Gene::GeneStructure object
\& Args    : None
.Ve
.SS "_add_exon"
.IX Subsection "_add_exon"
.Vb 6
\& Title   : _add_exon
\& Usage   : $obj\->_add_exon($gene, $transcript, ... exon data ...)
\& Function: Adds a new exon to both gene and transcript from the data
\&         : supplied as args
\& Example :
\& Returns : Nothing
.Ve
.SS "_set_strand"
.IX Subsection "_set_strand"
.Vb 7
\& Title   : _set_strand
\& Usage   : $obj\->_set_strand($gene)
\& Function: Sets the overall gene strand to the same strand as all
\&         : the exons if they are all on the same strand, or to strand 0
\&         : if the exons are on different strands.
\& Example :
\& Returns : Nothing
.Ve
.SS "_target_id"
.IX Subsection "_target_id"
.Vb 5
\& Title   : _target_id
\& Usage   : $obj\->_target_id
\& Function: get/set for genomic sequence id
\& Example :
\& Returns : A target ID
.Ve