Bio::Tools::Eponine man page on Pidora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Pidora logo
[printable version]

Bio::Tools::Eponine(3)User Contributed Perl DocumentatioBio::Tools::Eponine(3)

NAME
       Bio::Tools::Eponine - Results of one Eponine run

SYNOPSIS
	use Bio::Tools::Eponine;
	use strict;
	   my $seq = "/data/seq.fa";
	   my $threshold  = "0.999";
	   my @params = ( -seq => $seq,
			  -threshold => $threshold);

	  my $factory = Bio::Tools::Run::Eponine->new(@params);
	    # run eponine against fasta
	       my $r = $factory->run_eponine($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->seq_id. "\n";
		      }
	      }

DESCRIPTION
       Parser for Eponine, a probabilistic transcription start site detector
       optimized for mammalian genomic sequence. This module inherits off
       Bio::Tools::AnalysisResult and therefore implements
       Bio::SeqAnalysisParserI (see Bio::Tools::AnalysisResult and
       Bio::SeqAnalysisParserI).

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 - Tania Oh
       <gisoht-at-nus.edu.sg>

APPENDIX
       The rest of the documentation details each of the object methods.
       Internal methods are usually preceded with a _

   analysis_method
	Usage	  : $mzef->analysis_method();
	Purpose	  : Inherited method. Overridden to ensure that the name matches
		    /mzef/i.
	Returns	  : String
	Argument  : n/a

   next_feature
	Title	: next_feature
	Usage	: while($gene = $mzef->next_feature()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the MZEF 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.

		  Note that with the present version of MZEF there will only be one
		  object returned, because MZEF does not predict individual genes
		  but just potential internal exons.
	Example :
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	:

   next_prediction
	Title	: next_prediction
	Usage	: while($gene = $mzef->next_prediction()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the MZEF result
		  file. Call this method repeatedly until FALSE is returned.

		  Note that with the present version of MZEF there will only be one
		  object returned, because MZEF does not predict individual genes
		  but just potential internal exons.
	Example :
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	:

   _parse_predictions
	Title	: _parse_predictions()
	Usage	: $obj->_parse_predictions()
	Function: Parses the prediction section. Automatically called by
		  next_prediction() if not yet done.
	Example :
	Returns :

   create_feature
	   Title   :   create_feature
	   Usage   :   obj->create_feature($feature)
	   Function:   Returns an array of features
	   Returns :   Returns an array of features
	   Args	   :   none

   _prediction
	Title	: _prediction()
	Usage	: $gene = $obj->_prediction()
	Function: internal
	Example :
	Returns :

   _predictions_parsed
	Title	: _predictions_parsed
	Usage	: $obj->_predictions_parsed
	Function: internal
	Example :
	Returns : TRUE or FALSE

perl v5.14.1			  2011-07-22		Bio::Tools::Eponine(3)
[top]

List of man pages available for Pidora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net