GO::Model::Evidence;
my $ev_l = $association->evidence_list; foreach my $ev (@$ev_l) { print "Evidence for association %s : %s\n", $association->gene_product->symbol, $ev->code; }
evidence for an association
see http://www.geneontology.org/GO.evidence.html for a list of evidence codes
Usage - $ev->code("IEA"); Returns - Args -
gets/sets the evidence code
see http://www.geneontology.org/GO.evidence.html
Usage - Returns - Args -
gets/sets the sequence accesion GO::Model::Xref
ALPHA CODE - API may change
used to set the GO::Model::Xref list from a text string. eg
$ev->seq_acc("SGD:RRP41; SGDID:L0003550");
will actually add two GO::Model::Xref objects
This method doesnt really belong in the GO::Model::* hierarchy as it contains parsing code. Its a minor hack mainly due to the fact that this data is still denormalized in the database.
equivalent to WITH column in gene_association files, and evidence_dbxref tables in db
gets/sets the literature or sequence reference GO::Model::Xref
NOTE: at some point we may want to deprecate this method and persuade API client code to call
$ev->literature_xref
instead, to make explicit the fact that this is a literature reference as opposed to a sequence reference
Usage - Returns - GO::Model::Xref listref Args -
returns all (sequence and literature) references
deprected - sets first pub_xref_list
Usage - print join("; ", GO::Model::Evidence->valid_codes); Returns - string array Args -
list of valid evidence codes
To install GO::Utils, copy and paste the appropriate command in to your terminal.
cpanm
cpanm GO::Utils
CPAN shell
perl -MCPAN -e shell install GO::Utils
For more information on module installation, please visit the detailed CPAN module installation guide.