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

  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
  }

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

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 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')

 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)

 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)

 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)

 Usage     : $obj->analysis_method();
 Purpose   : Inherited method. Overridden to ensure that the name matches
             /ERPIN/i.
 Returns   : String
 Argument  : n/a

 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)

 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)

#
# BioPerl module for Bio::Tools::ERPIN
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Chris Fields <cjfields-at-uiuc-dot-edu>
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

# Let the code begin...

package Bio::Tools::ERPIN;
use strict;

use Bio::SeqFeature::Generic;

use base qw(Bio::Tools::AnalysisResult);

our($MotifTag,$SrcTag,$DescTag) = qw(misc_binding ERPIN erpin);

sub _initialize {
    my($self,@args) = @_;
    $self->warn('Use of this module is deprecated.  Use Bio::SearchIO::erpin instead');    
    $self->SUPER::_initialize(@args);
    my ($motiftag,$desctag,$srctag) =  $self->SUPER::_rearrange([qw(MOTIFTAG
                                                                    DESCTAG
                                                                    SRCTAG
                                   )],
                                    @args);
    $self->motif_tag(defined $motiftag ? $motiftag : $MotifTag);
    $self->source_tag(defined $srctag ? $srctag : $SrcTag);
    $self->desc_tag(defined $desctag ? $desctag : $DescTag);
    foreach (qw(_tset _tset_desc _cutoff _db _db_desc
               _db_ratios _eval_cutoff _seqid _secacc _seqdesc )) {
        $self->{$_}='';
    }
}

sub motif_tag{
    my $self = shift;

    return $self->{'motif_tag'} = shift if @_;
    return $self->{'motif_tag'};
}

sub source_tag{
    my $self = shift;

    return $self->{'source_tag'} = shift if @_;
    return $self->{'source_tag'};
}

sub desc_tag{
    my $self = shift;

    return $self->{'desc_tag'} = shift if @_;
    return $self->{'desc_tag'};
}

#-------------
sub analysis_method { 
#-------------
    my ($self, $method) = @_;  
    if($method && ($method !~ /ERPIN/i)) {
    $self->throw("method $method not supported in " . ref($self));
    }
    return $self->SUPER::analysis_method($method);
}

sub next_feature {
    my ($self,@args) = @_;
    # even though next_prediction doesn't expect any args (and this method
    # does neither), we pass on args in order to be prepared if this changes
    # ever
    return $self->next_prediction(@args);
}

sub next_prediction {
    my ($self) = @_;
    my ($motiftag,$srctag,$desctag) = ( $self->motif_tag,
                       $self->source_tag,
                       $self->desc_tag);
    # hit vars
    my ($strand, $start, $end, $sequence, $logodds, $score)=0;
    while($_ = $self->_readline) {
        #skip blank lines
        next if /^\s+$/;
        # parse header; there's probably a better way to do this, perhaps by
        # mapping, but this works for now...
        if(/^Training set:\s+\"(.*)\":$/) {
            $self->{'_tset'}=$1;
        }
        elsif(/\s+(\d+ sequences of length \d+)/){
            $self->{'_tset_descr'}=$1;
        }
        elsif(/^Cutoff:\s+(\S+)\s+$/) {
            $self->{'_cutoff'}=$1;
        }
        elsif(/^Database:\s+\"(.*)\"$/) {
            $self->{'_db'}=$1;
        }
        elsif(/^\s+(\d+ nucleotides to be processed in \d+ sequence)$/) {
            $self->{'_db_desc'}=$1;
        }
        elsif(/^\s+ATGC ratios:\s(\d.\d+)\s+(\d.\d+)\s+(\d.\d+)\s+(\d.\d+)$/) {
            my $atgc=sprintf("A=%0.3f T=%0.3f G=%0.3f C=%0.3f", $1, $2, $3, $4);
            $self->{'_db_ratios'}=$atgc;
        }
        elsif(/^E-value at cutoff \S+ for \S+(?:G|M|k)?b double strand data: (\S+)/) {
            $self->{'_eval_cutoff'}=$1;
        }
        # catch hit, store in private hash keys
        elsif (/^>(.*)/) {
            $self->{_seq_desc} = $1;
            if($self->{_seq_desc} =~
               /(?:P<db>gb|gi|emb|dbj|sp|pdb|bbs|ref|lcl)\|(\d+)((?:\:|\|)\w+\|(\S*.\d+)\|)?/) { 
                $self->{_seqid} = $1; # pulls out gid
                $self->{_seq_acc} = $3;
            } else {
                $self->{_seqid} = $self->{_seq_desc};
                $self->{_seq_acc} = '';
            }
        }
        # parse next hit
        elsif (/^(FW|RC)\s+\d+\s+(\d+)..(\d+)\s+(\d+.\d+)\s+(.*)/) {
            ($strand, $start, $end, $logodds, $score)=($1, $2, $3, $4, $5);
            $score =~ s/^e/1e/i;
            chomp ($sequence = $self->_readline); # grab next line, which is the sequence hit
            my $gene = Bio::SeqFeature::Generic->new(-seq_id => $self->{_seqid},
                                                      -start  => $start,
                                                      -end    => $end,
                                                      -strand => $strand eq 'FW' ? 1 : -1,
                                                      -score  => $score,
                                                      -primary_tag => $motiftag,
                                                      -source_tag  => $srctag,
                                                      -display_name => $desctag,
                                                      -tag     => {
                                                        'tset'          => $self->{_tset},
                                                        'tsetdesc'      => $self->{_tset_descr},
                                                        'cutoff'        => $self->{_cutoff},
                                                        'database'      => $self->{_db},
                                                        'dbdesc'        => $self->{_db_desc},
                                                        'dbratios'      => $self->{_db_ratios},
                                                        'descline'      => $self->{_seq_desc},
                                                        'accession'     => $self->{_seq_acc},
                                                        'logodds'       => $logodds,
                                                        'sequence'      => $sequence}
                                                    );
            return $gene;
        }
        #else {
        #    $self->debug("unrecognized line: $_");
        #}
    }
}

1;