Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic


         use Bio::Tools::Est2Genome;

         my $featureiter = Bio::Tools::Est2Genome->new(-file => 'output.est2genome');

         # This is going to be fixed to use the SeqAnalysisI next_feature
         # Method eventually when we have the objects to put the data in
         # properly
         while( my $f = $featureiter->parse_next_gene ) {
          # process Bio::SeqFeature::Generic objects here


       This module is a parser for "est2genome" [EMBOSS] alignments of est/cdna sequence to
       genomic DNA.  This is generally accepted as the best program for predicting splice sites
       based on est/dnas (as far as I know).

       This module currently does not try pull out the ungapped alignments (Segment) but may in
       the future.


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AUTHOR - Jason Stajich



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

        Title   : new
        Usage   : my $obj = Bio::Tools::Est2Genome->new();
        Function: Builds a new Bio::Tools::Est2Genome object
        Returns : an instance of Bio::Tools::Est2Genome
        Args    : -file => 'output.est2genome' or
                  -fh   => \*EST2GENOMEOUTPUT
                  -genomefirst => 1  # genome was the first input (not standard)

        Usage     : $sim4->analysis_method();
        Purpose   : Inherited method. Overridden to ensure that the name matches
        Returns   : String
        Argument  : n/a

        Title   : parse_next_gene
        Usage   : @gene = $est2genome_result->parse_next_gene;
                  foreach $exon (@exons) {
                      # do something

        Function: Parses the next alignments of the est2genome result file and
                  returns the found exons as an array of
                  Bio::SeqFeature::SimilarityPair objects. Call
                  this method repeatedly until an empty array is returned to get the
                  results for all alignments.

                  The $exon->seq_id() attribute will be set to the identifier of the
                  respective sequence for both sequences.
                  The length is accessible via the seqlength()
                  attribute of $exon->query() and
        Returns : An array (or array reference) of Bio::SeqFeature::SimilarityPair and Bio::SeqFeature::Generic objects
                  or Bio::SeqFeature::Gene::GeneStructure
        Args    : flag(1/0) indicating to return Bio::SeqFeature::Gene::GeneStructure or Bio::SeqFeature::SimilarityPair
                  defaults to 0

        Title   : next_feature
        Usage   : $seqfeature = $obj->next_feature();
        Function: Returns the next feature available in the analysis result, or
                  undef if there are no more features.
        Example :
        Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
                  more features.
        Args    : none