Bio::Tools ERPIN
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Summary
Bio::Tools::ERPIN - a parser for ERPIN output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::Generic
Inherit
Bio::Tools::AnalysisResult
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).
Methods
_initialize
No description
Code
motif_tagDescriptionCode
source_tagDescriptionCode
desc_tagDescriptionCode
analysis_methodDescriptionCode
next_featureDescriptionCode
next_predictionDescriptionCode
Methods description
motif_tagcode    nextTop
 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_tagcodeprevnextTop
 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_tagcodeprevnextTop
 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_methodcodeprevnextTop
 Usage     : $obj->analysis_method();
 Purpose   : Inherited method. Overridden to ensure that the name matches
             /ERPIN/i.
 Returns   : String
 Argument  : n/a
next_featurecodeprevnextTop
 Title   : next_feature
 Usage   : while($gene = $obj->next_feature()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the ERPIN result
           file. Call this method repeatedly until FALSE is returned.
           The returned object is actually a SeqFeatureI implementing object.
           This method is required for classes implementing the
           SeqAnalysisParserI interface, and is merely an alias for 
           next_prediction() at present.
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    : None (at present)
next_predictioncodeprevnextTop
 Title   : next_prediction
 Usage   : while($gene = $obj->next_prediction()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the ERPIN result
           file. Call this method repeatedly until FALSE is returned.
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    : None (at present)
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my($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 )) {
        $self->{$_}='';
    }
}
motif_tagdescriptionprevnextTop
sub motif_tag {
    my $self = shift;

    return $self->{'motif_tag'} = shift if @_;
    return $self->{'motif_tag'};
}
source_tagdescriptionprevnextTop
sub source_tag {
    my $self = shift;

    return $self->{'source_tag'} = shift if @_;
    return $self->{'source_tag'};
}
desc_tagdescriptionprevnextTop
sub desc_tag {
    my $self = shift;

    return $self->{'desc_tag'} = shift if @_;
    return $self->{'desc_tag'};
}
analysis_methoddescriptionprevnextTop
sub analysis_method {
 #-------------
    my ($self, $method) = @_;  
    if($method && ($method !~ /ERPIN/i)) {
    $self->throw("method $method not supported in " . ref($self));
    }
    return $self->SUPER::analysis_method($method);
}
next_featuredescriptionprevnextTop
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 $self->next_prediction(@args);
}
next_predictiondescriptionprevnextTop
sub next_prediction {
    my ($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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris FieldsTop
Email cjfields-at-uiuc-dot-edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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')