bio::tools::run::trnascanse(3pm) [debian man page]
Bio::Tools::Run::tRNAscanSE(3pm) User Contributed Perl Documentation Bio::Tools::Run::tRNAscanSE(3pm)NAME
Bio::Tools::Run::tRNAscanSE - Wrapper for local execution of tRNAscan-SE
SYNOPSIS
my $factory = Bio::Tools::Run::tRNAscanSE->new('-program' => 'tRNAscan-SE');
# Pass the factory Bio::Seq objects
# returns a Bio::Tools::tRNAscanSE object
my $factory = $factory->run($seq);
or
my $factory = $factory->run(@seq);
DESCRIPTION
Wrapper module for tRNAscan-SE.
tRNAscan-SE is open source and available at http://selab.wustl.edu/cgi-bin/selab.pl?mode=software#trnascan/ <http://selab.wustl.edu/cgi-
bin/selab.pl?mode=software#trnascan/>.
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 - Mark Johnson
Email: mjohnson-at-watson-dot-wustl-dot-edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
program_name
Title : program_name
Usage : $factory>program_name()
Function: gets/sets the program name
Returns: string
Args : string
program_dir
Title : program_dir
Usage : $factory->program_dir()
Function: gets/sets the program dir
Returns: string
Args : string
new
Title : new
Usage : $tRNAscanSE->new(@params)
Function: creates a new tRNAscanSE factory
Returns: Bio::Tools::Run::tRNAscanSE
Args :
run
Title : run
Usage : $obj->run($seq_file)
Function: Runs tRNAscan-SE
Returns : A Bio::Tools::tRNAscanSE object
Args : An array of Bio::PrimarySeqI objects
_run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : An instance of Bio::Tools::tRNAscanSE
Args : file name
_write_seq_file
Title : _write_seq_file
Usage : obj->_write_seq_file($seq) or obj->_write_seq_file(@seq)
Function: Internal(not to be used directly)
Returns : Name of a temp file containing program output
Args : One or more Bio::PrimarySeqI objects
perl v5.12.3 2011-06-18 Bio::Tools::Run::tRNAscanSE(3pm)
Check Out this Related Man Page
Bio::Tools::tRNAscanSE(3pm) User Contributed Perl Documentation Bio::Tools::tRNAscanSE(3pm)NAME
Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output
SYNOPSIS
use Bio::Tools::tRNAscanSE;
my $parser = Bio::Tools::tRNAscanSE->new(-file => 'result.tRNAscanSE');
# parse the results
while( my $gene = $parser->next_prediction ) {
@exon_arr = $gene->get_SeqFeatures();
}
DESCRIPTION
This script will parse tRNAscan-SE output. Just the tabular output of the tRNA locations in the genome for now.
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 the
Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Tools::tRNAscanSE->new();
Function: Builds a new Bio::Tools::tRNAscanSE object
Returns : an instance of Bio::Tools::tRNAscanSE
Args : -fh/-file for input filename
-genetag => primary tag used in gene features (default 'tRNA_gene')
-exontag => primary tag used in exon features (default 'tRNA_exon')
-srctag => source tag used in all features (default 'tRNAscan-SE')
gene_tag
Title : gene_tag
Usage : $obj->gene_tag($newval)
Function: Get/Set the value used for the 'gene_tag' of genes
Default is 'tRNA_gene' as set by the global $GeneTag
Returns : value of gene_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
source_tag
Title : source_tag
Usage : $obj->source_tag($newval)
Function: Get/Set the value used for the 'source_tag' of exons and genes
Default is 'tRNAscan-SE' as set by the global $SrcTag
Returns : value of source_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
exon_tag
Title : exon_tag
Usage : $obj->exon_tag($newval)
Function: Get/Set the value used for the 'primary_tag' of exons
Default is 'tRNA_exon' as set by the global $ExonTag
Returns : value of exon_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
analysis_method
Usage : $genscan->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/tRNAscan-SE/i.
Returns : String
Argument : n/a
next_feature
Title : next_feature
Usage : while($gene = $genscan->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Genscan result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::SeqFeature::Generic object.
Args :
See also : L<Bio::SeqFeature::Generic>
next_prediction
Title : next_prediction
Usage : while($gene = $genscan->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the Genscan result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : A Bio::SeqFeature::Generic object.
Args :
See also : L<Bio::SeqFeature::Generic>
perl v5.14.2 2012-03-02 Bio::Tools::tRNAscanSE(3pm)