.\" Automatically generated by Pod::Man 4.11 (Pod::Simple 3.35)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Bio::Tools::Genemark 3pm"
.TH Bio::Tools::Genemark 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.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Genemark \- Results of one Genemark run
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&   $Genemark = Bio::Tools::Genemark\->new(\-file => \*(Aqresult.Genemark\*(Aq);
\&   # filehandle:
\&   $Genemark = Bio::Tools::Genemark\->new( \-fh  => \e*INPUT );
\&
\&   # parse the results
\&   # note: this class is\-a Bio::Tools::AnalysisResult which implements
\&   # Bio::SeqAnalysisParserI, i.e., $Genemark\->next_feature() is the same
\&   while($gene = $Genemark\->next_prediction()) {
\&       # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
\&       # off Bio::SeqFeature::Gene::Transcript.
\&       #
\&       # $gene\->exons() returns an array of
\&       # Bio::Tools::Prediction::Exon objects
\&       # all exons:
\&       @exon_arr = $gene\->exons();
\&
\&       # initial exons only
\&       @init_exons = $gene\->exons(\*(AqInitial\*(Aq);
\&       # internal exons only
\&       @intrl_exons = $gene\->exons(\*(AqInternal\*(Aq);
\&       # terminal exons only
\&       @term_exons = $gene\->exons(\*(AqTerminal\*(Aq);
\&       # singleton exons:
\&       ($single_exon) = $gene\->exons();
\&   }
\&
\&   # essential if you gave a filename at initialization (otherwise the file
\&   # will stay open)
\&   $Genemark\->close();
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
The Genemark module provides a parser for Genemark gene structure
prediction output. It parses one gene prediction into a
Bio::SeqFeature::Gene::Transcript\- derived object.
.PP
This module has been developed around genemark.hmm for eukaryots v2.2a
and will probably not work with other versions.
.PP
This module also implements the Bio::SeqAnalysisParserI interface, and
thus can be used wherever such an object fits. See
Bio::SeqAnalysisParserI.
.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 \- Hilmar Lapp, Mark Fiers"
.IX Header "AUTHOR - Hilmar Lapp, Mark Fiers"
Email hlapp@gmx.net
      m.w.e.j.fiers@plant.wag\-ur.nl
.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 5
\& Title   : new
\& Usage   : my $obj = Bio::Tools::Genemark\->new();
\& Function: Builds a new Bio::Tools::Genemark object
\& Returns : an instance of Bio::Tools::Genemark
\& Args    : seqname
.Ve
.SS "analysis_method"
.IX Subsection "analysis_method"
.Vb 5
\& Usage     : $Genemark\->analysis_method();
\& Purpose   : Inherited method. Overridden to ensure that the name matches
\&             /GeneMark.hmm/i.
\& Returns   : String
\& Argument  : n/a
.Ve
.SS "next_feature"
.IX Subsection "next_feature"
.Vb 6
\& Title   : next_feature
\& Usage   : while($gene = $Genemark\->next_feature()) {
\&                  # do something
\&           }
\& Function: Returns the next gene structure prediction of the Genemark result
\&           file. Call this method repeatedly until FALSE is returned.
\&
\&           The returned object is actually a SeqFeatureI implementing object.
\&           This method is required for classes implementing the
\&           SeqAnalysisParserI interface, and is merely an alias for
\&           next_prediction() at present.
\&
\& Example :
\& Returns : A Bio::Tools::Prediction::Gene object.
\& Args    :
.Ve
.SS "next_prediction"
.IX Subsection "next_prediction"
.Vb 6
\& Title   : next_prediction
\& Usage   : while($gene = $Genemark\->next_prediction()) {
\&                  # do something
\&           }
\& Function: Returns the next gene structure prediction of the Genemark result
\&           file. Call this method repeatedly until FALSE is returned.
\&
\& Example :
\& Returns : A Bio::Tools::Prediction::Gene object.
\& Args    :
.Ve
.SS "_parse_predictions"
.IX Subsection "_parse_predictions"
.Vb 6
\& Title   : _parse_predictions()
\& Usage   : $obj\->_parse_predictions()
\& Function: Parses the prediction section. Automatically called by
\&           next_prediction() if not yet done.
\& Example :
\& Returns :
.Ve
.SS "_prediction"
.IX Subsection "_prediction"
.Vb 5
\& Title   : _prediction()
\& Usage   : $gene = $obj\->_prediction()
\& Function: internal
\& Example :
\& Returns :
.Ve
.SS "_add_prediction"
.IX Subsection "_add_prediction"
.Vb 5
\& Title   : _add_prediction()
\& Usage   : $obj\->_add_prediction($gene)
\& Function: internal
\& Example :
\& Returns :
.Ve
.SS "_predictions_parsed"
.IX Subsection "_predictions_parsed"
.Vb 5
\& Title   : _predictions_parsed
\& Usage   : $obj\->_predictions_parsed
\& Function: internal
\& Example :
\& Returns : TRUE or FALSE
.Ve
.SS "_has_cds"
.IX Subsection "_has_cds"
.Vb 5
\& Title   : _has_cds()
\& Usage   : $obj\->_has_cds()
\& Function: Whether or not the result contains the predicted CDSs, too.
\& Example :
\& Returns : TRUE or FALSE
.Ve
.SS "_read_fasta_seq"
.IX Subsection "_read_fasta_seq"
.Vb 7
\& Title   : _read_fasta_seq()
\& Usage   : ($id,$seqstr) = $obj\->_read_fasta_seq();
\& Function: Simple but specialised FASTA format sequence reader. Uses
\&           $self\->_readline() to retrieve input, and is able to strip off
\&           the traling description lines.
\& Example :
\& Returns : An array of two elements.
.Ve
.SS "_seqname"
.IX Subsection "_seqname"
.Vb 5
\& Title   : _seqname
\& Usage   : $obj\->_seqname($seqname)
\& Function: internal
\& Example :
\& Returns : String
.Ve