NAME

GO::Model::Evidence;

SYNOPSIS

my $ev_l = $association->evidence_list;
foreach my $ev (@$ev_l) {
  print "Evidence for association %s : %s\n",
    $association->gene_product->symbol,
    $ev->code;
}

DESCRIPTION

evidence for an association

see http://www.geneontology.org/GO.evidence.html for a list of evidence codes

code

Usage   - $ev->code("IEA");
Returns -
Args    -

gets/sets the evidence code

see http://www.geneontology.org/GO.evidence.html

seq_acc

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.

add_seq_xref

Usage   -
Returns -
Args    -

equivalent to WITH column in gene_association files, and evidence_dbxref tables in db

add_pub_xref

Usage   -
Returns -
Args    -

xref

Usage   -
Returns -
Args    -

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

xref_list

Usage   -
Returns - GO::Model::Xref listref
Args    -

returns all (sequence and literature) references

xref

Usage   -
Returns -
Args    -

deprected - sets first pub_xref_list

valid_codes

Usage   - print join("; ", GO::Model::Evidence->valid_codes);
Returns - string array
Args    -

list of valid evidence codes

cpanm GO::Utils

perl -MCPAN -e shell
install GO::Utils