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Bio::Tools::Spidey::ReUsersContributed Perl DocuBio::Tools::Spidey::Results(3)

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	   :

perl v5.24.1			  2017-07-08	Bio::Tools::Spidey::Results(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Ryan Golhar | APPENDIX

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