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://github.com/bioperl/bioperl-live/issues

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)