NAME

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

SYNOPSIS

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
}

DESCRIPTION

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.

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

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

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

APPENDIX

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

new

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)

analysis_method

Usage     : $sim4->analysis_method();
Purpose   : Inherited method. Overridden to ensure that the name matches
            /est2genome/i.
Returns   : String
Argument  : n/a

parse_next_gene

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
          $exon->est_hit().
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

next_feature

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