Bio::Tools::Spidey::Results(3pm)			User Contributed Perl Documentation			  Bio::Tools::Spidey::Results(3pm)

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), "
";

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

	       # $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(), "
";

	       foreach my $exon ( $exonset->sub_SeqFeature() ) {
		       # $exon is-a Bio::SeqFeature::FeaturePair
		       print "Exon from ", $exon->start, " to ", $exon->end,
			       " on strand ", $exon->strand(), "
";
		       # 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, "
";
	       }

	       # 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://redmine.open-bio.org/projects/bioperl/

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(), "
";
		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    :

perl v5.14.2							    2012-03-02					  Bio::Tools::Spidey::Results(3pm)