/ 
BioPerl-1.007000_003
River stage two • 61 direct dependents • 66 total dependents
/ Bio::Tools::Infernal

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://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::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)