| Bio::Tools::Run::Eponine(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Eponine(3pm) |
Bio::Tools::Run::Eponine - Object for execution of the Eponine which is a mammalian TSS predictor
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.
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.
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
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.
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/
Email gisoht@nus.edu.sg
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : java
Usage : $obj->java('/usr/opt/java130/bin/java');
Function: Get/set method for the location of java VM
Args : File path (optional)
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)
Title : threshold Usage : my $threshold = $self->threshold Function: Get/Set the threshold for Eponine Returns : string Args : b/w 0.9 and 1.0
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
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 :
Title : run_eponine
Usage : $obj->_run_eponine()
Function: execs the Java VM to run eponine
Returns : none
Args : none
| 2021-01-06 | perl v5.32.0 |