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Bio::Tools::ERPIN.3pm

NAME

Bio::Tools::ERPIN - a parser for ERPIN output

SYNOPSIS

   use Bio::Tools::ERPIN;
   my $parser = Bio::Tools::ERPIN->new( -file => $rna_output,
                                       -motiftag => 'protein_bind'
                                       -desctag => 'TRAP_binding');
   #parse the results
   while( my $motif = $parser->next_prediction) {
     # do something here
   }
 
 

DESCRIPTION

Parses raw ERPIN output.

This module is not currently complete. As is, it will parse raw ERPIN long format output and pack information into Bio::SeqFeature::Generic objects.

Several values have also been added in the 'tag' hash. These can be accessed using the following syntax:

   my ($entry) = $feature->get_Annotations('SecStructure');
 
 

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 ID 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

See t/ERPIN.t for example usage.

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 RNA secondary structural data).

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::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 'misc_binding')
            -desctag => tag used for display_name name (default 'erpin')
            -srctag  => source tag used in all features (default 'ERPIN')
 
 

motif_tag

  Title   : motiftag
  Usage   : $obj->motiftag($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 'ERPIN' 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 'erpin' 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)
 
 

analysis_method

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

next_prediction

  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)