/ 
BioPerl-1.007000_004
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::ERPIN

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:

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::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)