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.IX Title "Bio::Tools::Run::Eponine 3pm"
.TH Bio::Tools::Run::Eponine 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.
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.nh
.SH NAME
Bio::Tools::Run::Eponine \- Object for execution of the Eponine which
is a mammalian TSS predictor
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 8
\&  use Bio::Tools::Run::Eponine;
\&  use strict;
\&  my $seq = "/data/seq.fa";
\&  my $threshold  = "0.999";
\&  my @params = ( \*(Aq\-seq\*(Aq => $seq,
\&                 \*(Aq\-threshold\*(Aq => $threshold,
\&                 \*(Aq\-epojar\*(Aq  => \*(Aq/usr/local/bin/eponine\-scan.jar\*(Aq,
\&                  \*(Aq\-java\*(Aq  => \*(Aq/usr/local/bin/java\*(Aq);
\&
\&  my $factory = Bio::Tools::Run::Eponine\->new(@params);
\&  # run eponine against fasta
\&  my $r = $factory\->run($seq);
\&  my $parser = Bio::Tools::Eponine\->new($r);
\&
\&  while (my $feat = $parser\->next_prediction){
\&          #$feat contains array of SeqFeature
\&          foreach my $orf($feat){
\&                  print $orf\->seqname. "\en";
\&          }
\&  }
\&
\& # Various additional options and input formats are available.  See
\& # the DESCRIPTION section for details.
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
wrapper for eponine, a mammalian TSS predictor.
.PP
The environment variable EPONINEDIR must be set to point at either the
directory which contains eponine\-scan.jar or directly at the jar which
eponine-scan classfiles. NOTE: EPONINEDIR must point at the real file
not a symlink.
.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
.IX Header "AUTHOR"
Email gisoht@nus.edu.sg
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS java
.IX Subsection "java"
.Vb 4
\&    Title   :   java
\&    Usage   :   $obj\->java(\*(Aq/usr/opt/java130/bin/java\*(Aq);
\&    Function:   Get/set method for the location of java VM
\&    Args    :   File path (optional)
.Ve
.SS epojar
.IX Subsection "epojar"
.Vb 4
\&    Title   :   epojar
\&    Usage   :   $obj\->epojar(\*(Aq/some/path/to/eponine\-scan.jar\*(Aq);
\&    Function:   Get/set method for the location of the eponine\-scan executable JAR
\&    Args    :   Path (optional)
.Ve
.SS threshold
.IX Subsection "threshold"
.Vb 5
\& Title   : threshold
\& Usage   : my $threshold = $self\->threshold
\& Function: Get/Set the threshold for Eponine
\& Returns : string
\& Args    : b/w 0.9 and  1.0
.Ve
.SS run
.IX Subsection "run"
.Vb 5
\& Title   : run
\& Usage   : my @genes = $self\->run($seq)
\& Function: runs Eponine and creates an array of features
\& Returns : An Array of SeqFeatures
\& Args    : A Bio::PrimarySeqI
.Ve
.SS predict_TSS
.IX Subsection "predict_TSS"
.Vb 2
\& Title   : predict_TSS
\& Usage   : Alias for run()
.Ve
.SS \fB_setinput()\fP
.IX Subsection "_setinput()"
.Vb 6
\& Title   : _setinput
\& Usage   : Internal function, not to be called directly
\& Function: writes input sequence to file and return the file name
\& Example :
\& Returns : string
\& Args    :
.Ve
.SS _run_eponine
.IX Subsection "_run_eponine"
.Vb 5
\&    Title   :  run_eponine
\&    Usage   :   $obj\->_run_eponine()
\&    Function:   execs the Java VM to run eponine
\&    Returns :   none
\&    Args    :   none
.Ve