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

NAME

       Bio::Tools::Infernal - A parser for Infernal output

SYNOPSIS

	 use Bio::Tools::Infernal;
	 my $parser = Bio::Tools::Infernal->new(-file => $rna_output,
					       -motiftag => 'misc_binding'
					       -desctag => 'Lysine riboswitch',
					       -cm    => 'RF00168',
					       -rfam  =>  'RF00168',
					       -minscore => 20);
	 #parse the results, get a Bio::SeqFeature::FeaturePair
	 while( my $motif = $parser->next_prediction) {
	   # do something here
	 }

DESCRIPTION

       This is a highly experimental parser for Infernal output from the cmsearch program.  At some point it is anticipated that this will morph
       into a proper SearchIO parser, along with the related RNAMotif and ERPIN tools.

       The Infernal suite of programs are used for generating RNA CM (covariance models) and searching sequences using CMs to locate potentially
       similar structures.  The program is under active development; it is anticiapted that this will support the latest version available.

       This parser has been tested and is capable of parsing Infernal 0.7 and 0.71 output.  However, future Infernal versions may break parsing as
       the output is constantly evolving, so keep an eye on this space for additional notes.

       Currently data is parsed into a Bio::SeqFeature::FeaturePair object, consisting of a query (the covariance model) and the hit (sequence
       searched).

       Model data is accessible via the following:

	 Data		 SeqFeature::FeaturePair	 Note
	 --------------------------------------------------------------------------
	 primary tag	 $sf->primary_tag		 Rfam ID (if passed to new())
	 start		 $sf->start			 Based on CM length
	 end		 $sf->end			 Based on CM length
	 score		 $sf->score			 Bit score
	 strand 	 $sf->strand			 0 (CM does not have a strand)
	 seqid		 $sf->seq_id			 Rfam ID (if passed to new())
	 display name	 $sf->feature1->display_name	 CM name (if passed to new())
	 source 	 $sf->feature1->source tag	'Infernal' followed by version

       Hit data is accessible via the following:

	 Data		 SeqFeature::FeaturePair	 Note
	 ------------------------------------------------------------------
	 start		 $sf->hstart
	 end		 $sf->hend
	 score(bits)	 $sf->hscore
	 strand 	 $sf->hstrand
	 seqid		 $sf->hseqid
	 Primary Tag	 $sf->hprimary_tag
	 Source Tag	 $sf->hsource_tag

       Added FeaturePair tags are :

	  secstructure - entire description line (in case the regex used for
			 sequence ID doesn't adequately catch the name
	  model        - name of the descriptor file (may include path to file)
	  midline      - contains structural information from the descriptor
			 used as a query
	  hit	       - sequence of motif, separated by spaces according to
			 matches to the structure in the descriptor (in
			 SecStructure).
	  seqname      - raw sequence name (for downstream parsing if needed)

       An additional parameter ('minscore') is added due to the huge number of spurious hits generated by cmsearch.  This screens data, only
       building and returning objects when a minimal bitscore is present.

       See t/rnamotif.t for example usage.

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::Infernal->new();
	Function: Builds a new Bio::Tools::Infernal object
	Returns : an instance of Bio::Tools::Infernal
	Args	: -fh/-file  - for input filehandle/filename
		  -motiftag  - primary tag used in gene features (default 'misc_binding')
		  -desctag   - tag used for display_name name (default 'infernal')
		  -srctag    - source tag used in all features (default 'Infernal')
		  -rfam      - Rfam id number
		  -cm	     - covariance model used in analysis (may be same as rfam #)
		  -minscore  - minimum score (simple screener, since Infernal generates
			       a ton of spurious hits)
		  -version   - Infernal program version

   motif_tag
	Title	: motif_tag
	Usage	: $obj->motif_tag($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 'Infernal' 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 'infernal' 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 Infernal output, this should
		  be set every time an Infernal object is instantiated for clarity
	Returns : value of exon_tag (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   covariance_model
	Title	: covariance_model
	Usage	: $obj->covariance_model($newval)
	Function: Get/Set the value used for the covariance model used in the analysis.
	Returns : value of exon_tag (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   rfam
	Title	: rfam
	Usage	: $obj->rfam($newval)
	Function: Get/Set the Rfam accession number
	Returns : value of exon_tag (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   minscore
	Title	: minscore
	Usage	: $obj->minscore($newval)
	Function: Get/Set the minimum score threshold for generating SeqFeatures
	Returns : value of exon_tag (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   program_version
	Title	: program_version
	Usage	: $obj->program_version($newval)
	Function: Get/Set the Infernal program version
	Returns : value of exon_tag (a scalar)
	Args	: on set, new value (a scalar or undef, optional)
		  Note: this is set to $DEFAULT_VERSION by, um, default

   analysis_method
	Usage	  : $obj->analysis_method();
	Purpose   : Inherited method. Overridden to ensure that the name matches
		    /Infernal/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 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)

   next_prediction
	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)

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