NAME¶
Bio::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://redmine.open-bio.org/projects/bioperl/
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()
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