NAME

Bio::Tools::Spidey::Results - Results of a Spidey run

SYNOPSIS

   use Bio::Tools::Spidey::Results;
        my $spidey = Bio::Tools::Spidey::Results->new(-file => 'result.spidey' );

        # or

        my $spidey = Bio::Tools::Spidey::Results->new( -fh   => \*INPUT );

        # get the exons before doing anything else
        my $exonset = $spidey->next_exonset();

        # parse the results
        my @exons = $exonset->sub_SeqFeature();
        print "Total no of Exons: ", scalar(@exons), "\n";

        print "Genomic sequence length: ", $spidey->genomic_dna_length(), "\n";

        # $exonset is-a Bio::SeqFeature::Generic with Bio::Tools::Spidey::Exons
        # as sub features
        print "Delimited on sequence ", $exonset->seq_id(), " from ", 
                $exonset->start(), " to ", $exonset->end(), "\n";

        foreach my $exon ( $exonset->sub_SeqFeature() ) {
                # $exon is-a Bio::SeqFeature::FeaturePair
                print "Exon from ", $exon->start, " to ", $exon->end, 
                        " on strand ", $exon->strand(), "\n";
                # you can get out what it matched using the est_hit attribute
                my $homol = $exon->est_hit();
                print "Matched to sequence ", $homol->seq_id, 
                        " at ", $homol->start," to ", $homol->end, "\n";
        }

        # essential if you gave a filename at initialization (otherwise 
        # the file stays open)
        $spidey->close();

DESCRIPTION

The spidey module provides a parser and results object for spidey output. The spidey results are specialised types of SeqFeatures, meaning you can add them to AnnSeq objects fine, and manipulate them in the "normal" seqfeature manner.

The spidey Exon objects are Bio::SeqFeature::FeaturePair inherited objects. The $esthit = $exon->est_hit() is the alignment as a feature on the matching object (normally, a cDNA), in which the start/end points are where the hit lies.

To make this module work sensibly you need to run

     spidey -i genomic.fasta -m cDNA.fasta

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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ryan Golhar

Email golharam@umdnj.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

analysis_method

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

parse_next_alignment

 Title   : parse_next_alignment
 Usage   : @exons = $spidey_result->parse_next_alignment;
           foreach $exon (@exons) {
               # do something
           }
 Function: Parses the next alignment of the Spidey result file and returns the
           found exons as an array of Bio::Tools::Spidey::Exon objects. Call
           this method repeatedly until an empty array is returned to get the
           results for all alignments.
 Example :
 Returns : An array of Bio::Tools::Spidey::Exon objects
 Args    :

next_exonset

  Title   : next_exonset
  Usage   : $exonset = $spidey_result->parse_next_exonset;
         print "Exons start at ", $exonset->start(), 
        "and end at ", $exonset->end(), "\n";
         for $exon ($exonset->sub_SeqFeature()) {
            # do something
         }
  Function: Parses the next alignment of the Spidey result file and returns the
       set of exons as a container of features. The container is itself
       a Bio::SeqFeature::Generic object, with the Bio::Tools::Spidey::Exon
       objects as sub features. Start, end, and strand of the container
       will represent the total region covered by the exons of this set.

      See the documentation of parse_next_alignment() for further
      reference about parsing and how the information is stored.
 Example : 
 Returns : An Bio::SeqFeature::Generic object holding Bio::Tools::Spidey::Exon
          objects as sub features.
 Args    :

next_feature

  Title   : next_feature
  Usage   : while($exonset = $spidey->next_feature()) {
            # do something
           }
  Function: Does the same as L<next_exonset()>. See there for documentation of
      the functionality. 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_exonset() at present.

  Example :
  Returns : A Bio::SeqFeature::Generic object.
  Args    :

genomic_dna_length

    Title   : genomic_dna_length
    Usage   : $spidey->genomic_dna_length();
    Function: Returns the length of the genomic DNA used in this Spidey result
    Example :
    Returns : An integer value.
    Args    :

splicesites

    Title   : splicesites
    Usage   : $spidey->splicesites();
    Function: Returns the number of splice sites found in this Spidey result
    Example :
    Returns : An integer value.
    Args    :

est_coverage

    Title   : est_coverage
    Usage   : $spidey->est_coverage();
    Function: Returns the percent of est coverage in this Spidey result
    Example :
    Returns : An integer value.
    Args    :

overall_percentage_id

    Title   : overall_percentage_id
    Usage   : $spidey->overall_percentage_id();
    Function: Returns the overall percent id in this Spidey result
    Example :
    Returns : An float value.
    Args    :

missing_mrna_ends

    Title   : missing_mrna_ends
    Usage   : $spidey->missing_mrna_ends();
    Function: Returns left/right/neither from Spidey
    Example :
    Returns : A string value.
    Args    :