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.\" ========================================================================
.\"
.IX Title "Bio::Tools::ERPIN 3pm"
.TH Bio::Tools::ERPIN 3pm "2014-07-13" "perl v5.18.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tools::ERPIN \-  a parser for ERPIN output
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 8
\&  use Bio::Tools::ERPIN;
\&  my $parser = Bio::Tools::ERPIN\->new( \-file => $rna_output,
\&                                      \-motiftag => \*(Aqprotein_bind\*(Aq
\&                                      \-desctag => \*(AqTRAP_binding\*(Aq);
\&  #parse the results
\&  while( my $motif = $parser\->next_prediction) {
\&    # do something here
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Parses raw \s-1ERPIN\s0 output.
.PP
This module is not currently complete.  As is, it will parse raw
\&\s-1ERPIN\s0 long format output and pack information into
Bio::SeqFeature::Generic objects.
.PP
Several values have also been added in the 'tag' hash.  These can be
accessed using the following syntax:
.PP
.Vb 1
\&  my ($entry) = $feature\->get_Annotations(\*(AqSecStructure\*(Aq);
.Ve
.PP
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 \s-1ID\s0 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
.PP
See t/ERPIN.t for example usage.
.PP
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 \s-1RNA\s0 secondary structural
data).
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Chris Fields"
.IX Header "AUTHOR - Chris Fields"
Email cjfields-at-uiuc-dot-edu
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 8
\& 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 \*(Aqmisc_binding\*(Aq)
\&           \-desctag => tag used for display_name name (default \*(Aqerpin\*(Aq)
\&           \-srctag  => source tag used in all features (default \*(AqERPIN\*(Aq)
.Ve
.SS "motif_tag"
.IX Subsection "motif_tag"
.Vb 10
\& Title   : motiftag
\& Usage   : $obj\->motiftag($newval)
\& Function: Get/Set the value used for \*(Aqmotif_tag\*(Aq, which is used for setting the
\&           primary_tag.
\&           Default is \*(Aqmisc_binding\*(Aq as set by the global $MotifTag.
\&           \*(Aqmisc_binding\*(Aq 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 (\*(Aqmisc_RNA\*(Aq, \*(Aqprotein_binding\*(Aq, \*(AqtRNA\*(Aq, 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)
.Ve
.SS "source_tag"
.IX Subsection "source_tag"
.Vb 6
\& Title   : source_tag
\& Usage   : $obj\->source_tag($newval)
\& Function: Get/Set the value used for the \*(Aqsource_tag\*(Aq.
\&           Default is \*(AqERPIN\*(Aq as set by the global $SrcTag
\& Returns : value of source_tag (a scalar)
\& Args    : on set, new value (a scalar or undef, optional)
.Ve
.SS "desc_tag"
.IX Subsection "desc_tag"
.Vb 10
\& 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 \*(Aq\-display_name\*(Aq.  Default is \*(Aqerpin\*(Aq 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)
.Ve
.SS "analysis_method"
.IX Subsection "analysis_method"
.Vb 5
\& Usage     : $obj\->analysis_method();
\& Purpose   : Inherited method. Overridden to ensure that the name matches
\&             /ERPIN/i.
\& Returns   : String
\& Argument  : n/a
.Ve
.SS "next_feature"
.IX Subsection "next_feature"
.Vb 12
\& Title   : next_feature
\& Usage   : while($gene = $obj\->next_feature()) {
\&                  # do something
\&           }
\& Function: Returns the next gene structure prediction of the ERPIN result
\&           file. Call this method repeatedly until FALSE is returned.
\&           The returned object is actually a SeqFeatureI implementing object.
\&           This method is required for classes implementing the
\&           SeqAnalysisParserI interface, and is merely an alias for 
\&           next_prediction() at present.
\& Returns : A Bio::Tools::Prediction::Gene object.
\& Args    : None (at present)
.Ve
.SS "next_prediction"
.IX Subsection "next_prediction"
.Vb 8
\& Title   : next_prediction
\& Usage   : while($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)
.Ve