Bio::Tools::Geneid - Results of one geneid run use Bio::Tools::Geneid; my $gid = Bio::Tools::Geneid(-file => "geneid.out"); while (my $gene = $gid->next_prediction) { my @transcripts = $gene->transcripts; foreach my $t (@transcripts) { my @exons = $t->exons; foreach my $e (@exons) { printf("Exon %d..%d\n", $e->start, $e->end); } } } This is the parser for the output of geneid by Enrique Blanco and Roderic Guigó (IMIM-UPF). See http://www1.imim.es/software/geneid. It relies on native geneid output format internally and will work with geneid versions 1.0 and 1.1. Currently this module supports only the default mode of operation which is to predict exons and assemble an optimal gene prediction. It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object.

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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email: kdj@sanger.ac.uk The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : $obj->new(-file = "<geneid.out"); $obj->new(-fh => \*GI); Function: Constructor for geneid wrapper. Takes either a file : or filehandle Returns : L<Bio::Tools::Geneid>

next_prediction
Title : next_prediction Usage : while($gene = $geneid->next_prediction) { # do something } Function: Returns the gene structure prediction of the geneid result file. Call this method repeatedly until FALSE is returned. Returns : A Bio::SeqFeature::Gene::GeneStructure object Args : None

_add_exon
Title : _add_exon Usage : $obj->_add_exon($gene, $transcript, ... exon data ...) Function: Adds a new exon to both gene and transcript from the data : supplied as args Example : Returns : Nothing

_set_strand
Title : _set_strand Usage : $obj->_set_strand($gene) Function: Sets the overall gene strand to the same strand as all : the exons if they are all on the same strand, or to strand 0 : if the exons are on different strands. Example : Returns : Nothing

_target_id
Title : _target_id Usage : $obj->_target_id Function: get/set for genomic sequence id Example : Returns : A target ID