NAME¶
Bio::Tools::Run::Glimmer - Wrapper for local execution of Glimmer, GlimmerM and
GlimmerHMM.
SYNOPSIS¶
# glimmer2
my $factory =
Bio::Tools::Run::Glimmer->new('-program' => 'glimmer3',
'-model' => 'model.icm');
# glimmer3
my $factory =
Bio::Tools::Run::Glimmer->new('-program' => 'glimmer2',
'-model' => 'model.icm');
# glimmerm
my $factory =
Bio::Tools::Run::Glimmer->new('-program' => 'glimmerm');
# glimmerHMM
my $factory =
Bio::Tools::Run::Glimmer->new('-program' => 'glimmerHMM');
# Pass the factory Bio::Seq objects
# returns a Bio::Tools::Glimmer object
my $glimmer = $factory->run($seq);
or
my $glimmer = $factor->run(@seq);
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.
Glimmer is open source and available at
<
http://www.cbcb.umd.edu/software/glimmer/>.
GlimmerM is open source and available at
<
http://www.tigr.org/software/glimmerm/>.
GlimmerHMM is open source and available at
<
http://www.cbcb.umd.edu/software/GlimmerHMM/>.
Note that Glimmer 2.X will only process the first sequence in a fasta file (if
you
run() more than one sequence at a time, only the first will be
processed).
Note that Glimmer 3.X produces two output files. This module only passes the
.predict file to Bio::Tools::Glimmer.
FEEDBACK¶
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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support¶
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
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:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Mark Johnson¶
Email: mjohnson-at-watson-dot-wustl-dot-edu
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
program_name¶
Title : program_name
Usage : $factory>program_name()
Function: gets/sets the program name
Returns: string
Args : string
program_dir¶
Title : program_dir
Usage : $factory->program_dir()
Function: gets/sets the program dir
Returns: string
Args : string
model¶
Title : model
Usage : $factory>model()
Function: gets/sets the name of the model (icm) file
Returns: string
Args : string
new¶
Title : new
Usage : $glimmer->new(@params)
Function: creates a new Glimmer factory
Returns: Bio::Tools::Run::Glimmer
Args :
run¶
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
_run¶
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : An instance of Bio::Tools::Glimmer
Args : file name, sequence identifier (optional)
_write_seq_file¶
Title : _write_seq_file
Usage : obj->_write_seq_file($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