Bio::Tools::ERPIN(3pm)					User Contributed Perl Documentation				    Bio::Tools::ERPIN(3pm)

NAME

       Bio::Tools::ERPIN -  a parser for ERPIN output

SYNOPSIS

	 use Bio::Tools::ERPIN;
	 my $parser = Bio::Tools::ERPIN->new( -file => $rna_output,
					     -motiftag => 'protein_bind'
					     -desctag => 'TRAP_binding');
	 #parse the results
	 while( my $motif = $parser->next_prediction) {
	   # do something here
	 }

DESCRIPTION

       Parses raw ERPIN output.

       This module is not currently complete.  As is, it will parse raw ERPIN long format output and pack information into
       Bio::SeqFeature::Generic objects.

       Several values have also been added in the 'tag' hash.  These can be accessed using the following syntax:

	 my ($entry) = $feature->get_Annotations('SecStructure');

       Added tags are :
	  tset	       - training set used for the sequence
	  tsetdesc     - training set description line
	  cutoff       - cutoff value used
	  database     - name of database
	  dbdesc       - description of database
	  dbratios     - nucleotide ratios of database (used to calculate evalue)
	  descline     - entire description line (in case the regex used for
			 sequence ID doesn't adequately catch the name
	  accession    - accession number of sequence (if present)
	  logodds      - logodds score value
	  sequence     - sequence from hit, separated based on training set

       See t/ERPIN.t for example usage.

       At some point a more complicated feature object may be used to support this data rather than forcing most of the information into tag/value
       pairs in a SeqFeature::Generic.	This will hopefully allow for more flexible analysis of data (specifically RNA secondary structural data).

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 - Chris Fields
       Email cjfields-at-uiuc-dot-edu

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::ERPIN->new();
	Function: Builds a new Bio::Tools::ERPIN object
	Returns : an instance of Bio::Tools::ERPIN
	Args	: -fh/-file for input filename
		  -motiftag => primary tag used in gene features (default 'misc_binding')
		  -desctag => tag used for display_name name (default 'erpin')
		  -srctag  => source tag used in all features (default 'ERPIN')

   motif_tag
	Title	: motiftag
	Usage	: $obj->motiftag($newval)
	Function: Get/Set the value used for 'motif_tag', which is used for setting the
		  primary_tag.
		  Default is 'misc_binding' as set by the global $MotifTag.
		  'misc_binding' is used here because a conserved RNA motif is capable
		  of binding proteins (regulatory proteins), antisense RNA (siRNA),
		  small molecules (riboswitches), or nothing at all (tRNA,
		  terminators, etc.).  It is recommended that this be changed to other
		  tags ('misc_RNA', 'protein_binding', 'tRNA', etc.) where appropriate.
		  For more information, see:
		  http://www.ncbi.nlm.nih.gov/collab/FT/index.html
	Returns : value of motif_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'.
		  Default is 'ERPIN' as set by the global $SrcTag
	Returns : value of source_tag (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   desc_tag
	Title	: desc_tag
	Usage	: $obj->desc_tag($newval)
	Function: Get/Set the value used for the query motif.  This will be placed in
		  the tag '-display_name'.  Default is 'erpin' as set by the global
		  $DescTag.  Use this to manually set the descriptor (motif searched for).
		  Since there is no way for this module to tell what the motif is from the
		  name of the descriptor file or the ERPIN output, this should
		  be set every time an ERPIN object is instantiated for clarity
	Returns : value of exon_tag (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

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

   next_feature
	Title	: next_feature
	Usage	: while($gene = $obj->next_feature()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the ERPIN 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.
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	: None (at present)

   next_prediction
	Title	: next_prediction
	Usage	: while($gene = $obj->next_prediction()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the ERPIN result
		  file. Call this method repeatedly until FALSE is returned.
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	: None (at present)

perl v5.14.2							    2012-03-02						    Bio::Tools::ERPIN(3pm)