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.\" ========================================================================
.\"
.IX Title "Bio::Tools::RNAMotif 3pm"
.TH Bio::Tools::RNAMotif 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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.nh
.SH "NAME"
Bio::Tools::RNAMotif \- A parser for RNAMotif output
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 8
\&  use Bio::Tools::RNAMotif;
\&  my $parser = Bio::Tools::RNAMotif\->new(\-file => $rna_output,
\&                                        \-motiftag => \*(Aqprotein_bind\*(Aq
\&                                        \-desctag => \*(AqTRAP_binding\*(Aq);
\&  #parse the results
\&  while( my $motif = $parser\->next_prediction) {
\&    # do something here
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Parses raw RNAMotif output.  RNAMotif uses a \s-1RNA\s0 profile, consisting
of sequence and structural elements stored in a descriptor file, to
search for potential motifs in a \s-1DNA\s0 sequence file.  For more
information, see:
.PP
Macke \s-1TJ,\s0 Ecker \s-1DJ,\s0 Gutell \s-1RR,\s0 Gautheret D, Case \s-1DA,\s0 Sampath R. 
RNAMotif, an \s-1RNA\s0 secondary structure definition and search algorithm.
Nucleic Acids Res. 2001 Nov 15;29(22):4724\-35. 
http://www.scripps.edu/mb/case/casegr\-sh\-3.5.html.
.PP
This module is not currently complete.  As is, it will parse raw
RNAMotif output (i.e. information not passed through the secondary
programs rmfmt or rm2ct) and pack information into
Bio::SeqFeature::Generic objects.  Currently, parsing extra output
utilized by the \fIsprintf()\fR function in an RNAMotif descriptor is not
implemented; this information is instead packed into the score tag,
which can be accessed by using the following:
.PP
.Vb 1
\&  my ($score) = $feature\->score;
.Ve
.PP
If the score contains anything besides a digit, it will throw a
warning that \fIsprintf()\fR may have been used.
Several values have also been added in the 'tag' hash.  These can be
accessed using the following syntax:
.PP
.Vb 1
\&  my ($entry) = $feature\->get_Annotations(\*(Aqsecstructure\*(Aq);
.Ve
.PP
Added tags are :
.PP
.Vb 8
\&   descline     \- entire description line (in case the regex used for
\&                  sequence ID doesn\*(Aqt adequately catch the name
\&   descfile     \- name of the descriptor file (may include path to file)
\&   secstrucure  \- contains structural information from the descriptor
\&                  used as a query
\&   sequence     \- sequence of motif, separated by spaces according to
\&                  matches to the structure in the descriptor (in
\&                  SecStructure).
.Ve
.PP
See t/RNAMotif.t for example usage.
.PP
The clean_features method can also be used to return a list of seqfeatures (in a
Bio::SeqFeature::Collection object) that are within a particular region.   RNAMotif
is prone with some descriptors to returning redundant hits; an attempt to rectify
this problem is attempted with RNAMotif's companion program rmprune, which returns
the structure with the longest helices (and theoretically the best scoring structure).
However, this doesn't take into account alternative foldings which may score better.
This method adds a bit more flexibility, giving the user the ability to screen folds
based on where the feature is found and the score.  Passing a positive integer x
screens SeqFeatures based on the highest score within x bp, while a negative integer
screens based on the lowest score. So, to return the highest scoring values within
20 bp (likely using an arbitrary scroing system in the \s-1SCORE\s0 section of a descriptor
file), one could use:
.PP
.Vb 1
\&  $list = $obj\->clean_features(20);
.Ve
.PP
\&... and returning the lowest scoring structures within the same region (when the
score is based on calculated free energies from efn2) can be accomplished
by the following:
.PP
.Vb 1
\&  $list = $obj\->clean_features(\-20);
.Ve
.PP
If you wanted the best feature in a sequence, you could set this to a large number,
preferrably on that exceeds the bases in a sequence
.PP
.Vb 1
\&  $list = $obj\->clean_features(10000000);
.Ve
.PP
Each seqfeature in the collection can then be acted upon:
.PP
.Vb 4
\&  @sf = $list\->get_all_features;
\&  for my $f (@sf) {
\&    # do crazy things here
\&  }
.Ve
.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).  It works for now...
.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::RNAMotif\->new();
\& Function: Builds a new Bio::Tools::RNAMotif object 
\& Returns : an instance of Bio::Tools::RNAMotif
\& 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 \*(Aqrnamotif\*(Aq)
\&           \-srctag  => source tag used in all features (default \*(AqRNAMotif\*(Aq)
.Ve
.SS "motif_tag"
.IX Subsection "motif_tag"
.Vb 10
\& Title   : motif_tag
\& Usage   : $obj\->motif_tag($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 \*(AqRNAMotif\*(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 \*(Aqrnamotif\*(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 RNAMotif output, this should
\&           be set every time an RNAMotif 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     : $obj\->analysis_method();
\& Purpose   : Inherited method. Overridden to ensure that the name matches
\&             /RNAMotif/i.
\& Returns   : String
\& Argument  : n/a
.Ve
.SS "next_feature"
.IX Subsection "next_feature"
.Vb 12
\& Title   : next_feature
\& Usage   : while($gene = $obj\->next_feature()) {
\&                  # do something
\&           }
\& Function: Returns the next gene structure prediction of the RNAMotif result
\&           file. Call this method repeatedly until FALSE is returned.
\&           The returned object is actually a SeqFeatureI implementing object.
\&           This method is required for classes implementing the
\&           SeqAnalysisParserI interface, and is merely an alias for 
\&           next_prediction() at present.
\& Returns : A Bio::Tools::Prediction::Gene object.
\& Args    : None (at present)
.Ve
.SS "next_prediction"
.IX Subsection "next_prediction"
.Vb 8
\& Title   : next_prediction
\& Usage   : while($gene = $obj\->next_prediction()) {
\&                  # do something
\&           }
\& Function: Returns the next gene structure prediction of the RNAMotif result
\&           file. Call this method repeatedly until FALSE is returned.
\& Returns : A Bio::SeqFeature::Generic object
\& Args    : None (at present)
.Ve
.SS "clean_features"
.IX Subsection "clean_features"
.Vb 6
\& Title   : next_prediction
\& Usage   : @list = $obj\->clean_features(\-10);
\& Function: Cleans (reduces redundant hits) based on score, position
\& Returns : a Bio::SeqFeature::Collection object
\& Args    : Pos./Neg. integer (for highest/lowest scoring seqfeature within x bp).
\& Throws  : Error unless digit is entered.
.Ve