Bio::Tools::Geneid - Results of one geneid run
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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : $obj->new(-file = "<geneid.out");
$obj->new(-fh => \*GI);
Function: Constructor for geneid wrapper. Takes either a file
: or filehandle
Returns : L<Bio::Tools::Geneid>
Title : next_prediction
Usage : while($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
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
Returns : Nothing
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.
Returns : Nothing
Title : _target_id
Usage : $obj->_target_id
Function: get/set for genomic sequence id
Returns : A target ID
To install BioPerl, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell
For more information on module installation, please visit the detailed CPAN module installation guide.