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.IX Title "Bio::Tools::Run::Genscan 3pm"
.TH Bio::Tools::Run::Genscan 3pm 2024-04-27 "perl v5.38.2" "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::Run::Genscan \- Object for identifying genes in a
given sequence given a matrix(for appropriate organisms).
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 3
\&  # Build a Genscan factory
\&  my $param = (\*(AqMATRIX\*(Aq=>HumanIso.smat);
\&  my  $factory = Bio::Tools::Run::Genscan\->new($param);
\&
\&  # Pass the factory a Bio::Seq object
\&  #@genes is an array of Bio::Tools::Predictions::Gene objects
\&  my @genes = $factory\->run($seq);
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
Genscan is a gene identifying program developed by Christopher Burge
http://genes.mit.edu/burgelab/
.PP
By default it looks for an executable called \fIgenscan\fR and data/parameter files
in the directory specified by the \fIGENSCANDIR\fR environmental variable.
.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 \- Bala"
.IX Header "AUTHOR - Bala"
Email savikalpa@fugu\-sg.org
.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: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS program_dir
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS \fBpredict_genes()\fP
.IX Subsection "predict_genes()"
.Vb 5
\&    Title   :   predict_genes()
\&    Usage   :   DEPRECATED: use $obj\->run($seq) instead 
\&    Function:   Runs genscan and creates an array of Genes
\&    Returns :   An array of Bio::Tools::Prediction::Gene objects
\&    Args    :   A Bio::PrimarySeqI
.Ve
.SS run
.IX Subsection "run"
.Vb 5
\&    Title   :   run
\&    Usage   :   $obj\->run($seq)
\&    Function:   Runs genscan and creates an array of Genes
\&    Returns :   An array of Bio::Tools::Prediction::Gene objects
\&    Args    :   A Bio::PrimarySeqI
.Ve
.SS _run
.IX Subsection "_run"
.Vb 5
\&    Title   :   _run
\&    Usage   :   $obj\->_run()
\&    Function:   Internal(not to be used directly)
\&    Returns :   An array of Bio::Tools::Prediction::Gene objects
\&    Args    :
.Ve
.SS \fB_set_input()\fP
.IX Subsection "_set_input()"
.Vb 5
\&    Title   :   _set_input
\&    Usage   :   obj\->_set_input($matrixFile,$seqFile)
\&    Function:   Internal(not to be used directly)
\&    Returns :  
\&    Args    :
.Ve
.SS \fB_writeSeqFile()\fP
.IX Subsection "_writeSeqFile()"
.Vb 5
\&    Title   :   _writeSeqFile
\&    Usage   :   obj\->_writeSeqFile($seq)
\&    Function:   Internal(not to be used directly)
\&    Returns :   
\&    Args    :
.Ve