Bio::Tools::Infernal.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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)