Christopher Fields > BioPerl > Bio::Tools::Est2Genome



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Open  4
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Module Version: 1.006924   Source  


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


  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
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