Bio::Tools::Run::EponiUser)Contributed Perl DocumenBio::Tools::Run::Eponine(3)NAMEBio::Tools::Run::Eponine - Object for execution of the Eponine which is
a mammalian TSS predictor
SYNOPSIS
use Bio::Tools::Run::Eponine;
use strict;
my $seq = "/data/seq.fa";
my $threshold = "0.999";
my @params = ( '-seq' => $seq,
'-threshold' => $threshold,
'-epojar' => '/usr/local/bin/eponine-scan.jar',
'-java' => '/usr/local/bin/java');
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. "\n";
}
}
# Various additional options and input formats are available. See
# the DESCRIPTION section for details.
DESCRIPTION
wrapper for eponine, a mammalian TSS predictor.
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.
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://bugzilla.open-bio.org/
AUTHOR
Email gisoht@nus.edu.sg
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
java
Title : java
Usage : $obj->java('/usr/opt/java130/bin/java');
Function: Get/set method for the location of java VM
Args : File path (optional)
epojar
Title : epojar
Usage : $obj->epojar('/some/path/to/eponine-scan.jar');
Function: Get/set method for the location of the eponine-scan executable JAR
Args : Path (optional)
threshold
Title : threshold
Usage : my $threshold = $self->threshold
Function: Get/Set the threshold for Eponine
Returns : string
Args : b/w 0.9 and 1.0
run
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
predict_TSS
Title : predict_TSS
Usage : Alias for run()_setinput()
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 :
_run_eponine
Title : run_eponine
Usage : $obj->_run_eponine()
Function: execs the Java VM to run eponine
Returns : none
Args : none
perl v5.14.1 2011-07-21 Bio::Tools::Run::Eponine(3)
