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.IX Title "Bio::Tools::Run::Glimmer 3pm"
.TH Bio::Tools::Run::Glimmer 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::Tools::Run::Glimmer \- Wrapper for local execution of Glimmer,
GlimmerM and GlimmerHMM.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 11
\&  # glimmer2
\&  my $factory =
\&      Bio::Tools::Run::Glimmer\->new(\*(Aq\-program\*(Aq => \*(Aqglimmer3\*(Aq,
\&                                    \*(Aq\-model\*(Aq   => \*(Aqmodel.icm\*(Aq);
\&  # glimmer3
\&  my $factory =
\&      Bio::Tools::Run::Glimmer\->new(\*(Aq\-program\*(Aq => \*(Aqglimmer2\*(Aq,
\&                                    \*(Aq\-model\*(Aq   => \*(Aqmodel.icm\*(Aq);
\&  # glimmerm
\&  my $factory =
\&      Bio::Tools::Run::Glimmer\->new(\*(Aq\-program\*(Aq => \*(Aqglimmerm\*(Aq);
\&
\&  # glimmerHMM
\&  my $factory =
\&      Bio::Tools::Run::Glimmer\->new(\*(Aq\-program\*(Aq => \*(AqglimmerHMM\*(Aq);
\&
\&  # Pass the factory Bio::Seq objects
\&  # returns a Bio::Tools::Glimmer object
\&  my $glimmer = $factory\->run($seq);
\&  or
\&  my $glimmer = $factor\->run(@seq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Wrapper module for the Glimmer family of programs.  Should work with
all currently available flavors: Glimmer, GlimmerM and GlimmerHMM.
However, only Glimmer 2.X and 3.X have been tested.
.PP
Glimmer is open source and available at
<http://www.cbcb.umd.edu/software/glimmer/>.
.PP
GlimmerM is open source and available at
<http://www.tigr.org/software/glimmerm/>.
.PP
GlimmerHMM is open source and available at
<http://www.cbcb.umd.edu/software/GlimmerHMM/>.
.PP
Note that Glimmer 2.X will only process the first
sequence in a fasta file (if you \fBrun()\fR more than one
sequence at a time, only the first will be processed).
.PP
Note that Glimmer 3.X produces two output files.  This 
module only passes the .predict file to Bio::Tools::Glimmer.
.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
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Mark Johnson"
.IX Header "AUTHOR - Mark Johnson"
.Vb 1
\& Email: johnsonm\-at\-gmail\-dot\-com
.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 "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: gets/sets the program name
\& Returns:  string
\& Args    : string
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir()
\& Function: gets/sets the program dir
\& Returns:  string
\& Args    : string
.Ve
.SS "model"
.IX Subsection "model"
.Vb 5
\& Title   : model
\& Usage   : $factory>model()
\& Function: gets/sets the name of the model (icm) file
\& Returns:  string
\& Args    : string
.Ve
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : $glimmer\->new(@params)
\& Function: creates a new Glimmer factory
\& Returns:  Bio::Tools::Run::Glimmer
\& Args    :
.Ve
.SS "run"
.IX Subsection "run"
.Vb 5
\& Title   :   run
\& Usage   :   $obj\->run($seq_file)
\& Function:   Runs Glimmer/GlimmerM/GlimmerHMM
\& Returns :   A Bio::Tools::Glimmer object
\& Args    :   An array of Bio::PrimarySeqI objects
.Ve
.SS "_run"
.IX Subsection "_run"
.Vb 5
\& Title   :   _run
\& Usage   :   $obj\->_run()
\& Function:   Internal(not to be used directly)
\& Returns :   An instance of Bio::Tools::Glimmer 
\& Args    :   file name, sequence identifier (optional)
.Ve
.SS "_write_seq_file"
.IX Subsection "_write_seq_file"
.Vb 5
\& Title   :   _write_seq_file
\& Usage   :   obj\->_write_seq_file($seq) or obj\->_write_seq_file(@seq)
\& Function:   Internal(not to be used directly)
\& Returns :   Name of a temp file containing program output
\& Args    :   One or more Bio::PrimarySeqI objects
.Ve