Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects use Bio::Tools::Est2Genome; my $featureiter = new Bio::Tools::Est2Genome(-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/cdnas*. This module currently does not try pull out the ungapped alignments (Segment) but may in the future. * AFAIK

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/MailList.shtml - About the mailing lists

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 via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Tools::Est2Genome(); 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