go::model::graphiterator(3pm) [debian man page]
GO::Model::GraphIterator(3pm) User Contributed Perl Documentation GO::Model::GraphIterator(3pm) NAME
GO::Model::GraphIterator - Graph iterator SYNOPSIS
$it = $graph->create_iterator; # returns a GO::Model::GraphIterator object while (my $ni = $it->next_node_instance) { $depth = $ni->depth; $term = $ni->term; $reltype = $ni->parent_rel->type; printf "%s %8s Term = %s (%s) // depth=%d ", "----" x $depth, $reltype, $term->name, $term->public_acc, $depth; } DESCRIPTION
SEE ALSO
GO::Model::Graph GO::Model::GraphNodeInstance order Usage - $graphiter->order("breadth"); Returns - string Args - string gets/sets traversal order; breadth or depth; default is depth direction Usage - $graphiter->direction("up"); Returns - string Args - string gets/sets direction; default is "down" compact Usage - $graphiter->compact(1); Returns - bool Args - bool set this if you dont want relationships to be traversed twice; this gives a more compact tree representation of the graph reltype_filter Usage - $graphiter->reltype_filter(qw(is_a part_of)) Returns - array Args - array by default, all relationship types are treated as transitive, and will be traversed by the iterator sometimes you dont want to traverse all relations, even if they are transitive. For example, when answering the query "find all genes expressed in the embryo" you way want subtypes of embryo and parts of the embryo but not things that develop_from the embryo. For more details, see <http://sourceforge.net/mailarchive/forum.php?thread_id=9448679&forum_id=43082> reset_cursor Usage - Returns - Args - next_node Usage - Returns - GO::Model::Term Args - next_node_instance Usage - Returns - GO::Model::GraphNodeInstance Args - flatten Usage - Returns - Args - _sortby_pos_in_list Careful, this sort function work on Term objects, not GraphNodeInstance objects. Comparison is done by the name of the term. perl v5.14.2 2013-02-07 GO::Model::GraphIterator(3pm)
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GO::Model::Term(3pm) User Contributed Perl Documentation GO::Model::Term(3pm) NAME
GO::Model::Term - a term or concept in an ontology SYNOPSIS
# From a file use GO::Parser; my $parser = new GO::Parser({handler=>'obj'}); # create parser object $parser->parse("gene_ontology.obo"); # parse file -> objects my $graph = $parser->handler->graph; # get L<GO::Model::Graph> object my $term = $graph->get_term("GO:0001303"); # fetch a term by ID printf "Term %s %s ", $term->name, $term->acc; # From a GO Database (requires go-db-perl) my apph = GO::AppHandle->connect(-dbname=>$dbname); my $term = $apph->get_term({acc=>00003677}); printf "Term:%s (%s) Definition:%s Synonyms:%s ", $term->name, $term->public_acc, $term->definition, join(", ", @{$term->synonym_list}); DESCRIPTION
Represents an Ontology term; the same class is used for process, compartment and function currently, a Term is not aware of its Relationships; to find out how a term is related to other terms, use the a GO::Model::Graph object, which will give you the GO::Model::Relationship objects; for example $rels = $graph->get_parent_relationships($term->acc); SEE ALSO
GO::Model::Relationship GO::Model::Graph GO::Model::Xref GO::Model::Association NOTES
Like all the GO::Model::* classes, this uses accessor methods to get or set the attributes. by using the accessor method without any arguments gets the value of the attribute. if you pass in an argument, then the attribuet will be set according to that argument. for single-valued attributes # this sets the value of the attribute $my_object->attribute_name("my value"); # this gets the value of the attribute $my_value = $my_object->attribute_name(); for lists: # this sets the values of the attribute $my_object->attribute_name(@my_values); # this gets the values of the attribute $my_values = $my_object->attribute_name(); acc Usage - print $term->acc() Alias - public_acc Returns - Args - accessor: gets/sets GO ID/accession [as an integer] throws: exception if you try to pass in a non-integer if you want to use IDs in the format GO:0000nnn, then use the method public_acc() name Usage - print $term->name; Returns - Args - accessor: gets/sets "name" attribute subset_list Usage - foreach (@{$term->subset_list || []}) { printf " $_ " } Returns - list of strings Args - list of strings [optional] List of subset Accs for a term Subsets are also known as GO Slims in_subset Usage - if ($term->in_subset('goslim_prok'); Returns - bool Args - subset-name str Tests if the term belongs to a subset definition Usage - print $term->definition; Returns - Args - accessor: gets/sets "definition" attribute primary_xref Title : primary_xref Usage : Function: Example : Returns : GO::Model::Xref Args : The same as acc(), except the ID is returned as a GO::Model::Xref rather than a string comment Title : comment Usage : $obj->comment($newval) Function: Example : Returns : value of comment (a scalar) Args : on set, new value (a scalar or undef, optional) definition_dbxref_list Title : definition_dbxref_list Usage : $obj->definition_dbxref(@xrefs) Function: Example : Returns : definition_dbxref_list hashlist (of GO::Model::Xref) Args : on set, new values (GO::Model::Xref hashlist) GO::Model::Xref add_definition_dbxref - Usage : $term->add_definition_dbxref($xref); - Args : GO::Term::Xref GO::Model::Xref has_synonym Usage - if ($term->has_synonym("autotrophy") {...} Returns - bool Args - string add_synonym Usage - $term->add_synonym("calcineurin"); Usage - $term->add_synonym(@synonym_strings); Returns - Args - Adds a synonym; loses type information (the synonym type in blank) synonym_list Usage - my $syn_l = $term->synonym_list; Usage - $term->synonym_list([$syn1, $syn2]); Returns - arrayref Args - arrayref [optional] accessor: gets/set list of synonyms [array reference] each synonym is represented as a string - this method loses synonym typing information. If used as a setter, will set the type for each synonym to null add_synonym_by_type Usage - $term->add_synonym_by_type('exact', $syn); Returns - Args - synonyms_by_type Usage - $synstrs = $term->synonyms_by_type('exact'); Usage - $term->synonyms_by_type('exact', @exact_syns); Returns - arrayref of strings Args - type string, arrayref of strings [optional] in getter mode, gets a list of synonyms of a particular type in setter mode, sets a list of synonyms for a particular type alt_id_list Usage - my $syn_l = $term->alt_id_list; Usage - $term->alt_id_list([$syn1, $syn2]); Returns - arrayref Args - arrayref [optional] accessor: gets/set list of synonyms [array reference] add_alt_id Usage - $term->add_alt_id('GO:0000001'); Returns - Args - id string, or list of id strings namespace (INHERITED) Usage - print $term->namespace(); # getting the type Usage - $term->namespace("molecular_function"); # setting the type Alias - type Alias - term_type Alias - category Alias - ontology Returns - string representing type Args - string represnting type [optional] The OBO namespace for the GO::Model::Term or GO::Model::Relationship This method is inherited from the superclass set_namespace_by_code Usage - $term->set_namespace_by_code("P"); Returns - Args - String: M, P or C Currently the mapping is hardcoded ('F'=>'molecular_function', 'P'=>'biological_process', 'C'=>'cellular_component'); get_code_from_namespace Usage - $code = $term->get_code_from_namespace; Returns - String: M, P or F Args - String (if omitted will use current namespace) Returns the code for the current namespace (or any given namespace if supplied) add_dbxref - Usage : $term->add_dbxref($xref); - Args : GO::Term::Xref GO::Model::Xref dbxref_list - Usage : $term->dbxref_list($xref); - Args : optional listref of GO::Term::Xref - Returns : listref of GO::Term::Xref accessor: gets/sets list of dbxref [array reference] is_obsolete accessor: gets/set obsolete flag [boolean is_root accessor: gets/set is_root flag [boolean] TERM ASSOCIATION METHODS
association_list Usage - $assoc_l = $term->association_list Returns - arrayref of GO::Model::Association Args - arrayref of GO::Model::Association [optional] accessor: gets/set list of associations [array reference] if this is undefined, the datasource will be queried for the associations selected_association_list Usage - $assoc_l = $term->selected_association_list Returns - arrayref of GO::Model::Association Args - arrayref of GO::Model::Association [optional] accessor: gets list of SELECTED associations [array reference] [this method is only of use if you are using it in conjunction with GO::AppHandle in the go-db-perl distro] this in not the total list of all associations associated with a term; if the term was created via a query on products, this will include those associations GO::Model::Association add_association Usage - $term->add_association($assoc); Returns - Args - GO::Model::Association GO::Model::Association add_selected_association Usage - Returns - Args - GO::Model::Association association_hash returns associations as listref of unique GeneProduct objects GO::Model::Association get_all_associations Usage - my $al = $term->get_all_associations Returns - GO::Model::Association list Args - returns all associations for the term and the terms beneath it in the GO DAG same as $apph->get_all_associations($term) GO::Model::Association n_associations Usage - my $n = $term->n_associations Returns - Args - product_list Usage - $prods = $term->product_list Returns - L<GO::Model::GeneProduct> listref Args - Returns a reference to an array of gene products that are attached directly to this term. (if the products have not been fetched, this method will call $term->association_list, cache the results, and use the associations to build the product list. succeeding calls of product_list to this term will hence be faster) See GO::Model::GeneProduct deep_product_list Usage - Returns - GO::Model::GeneProduct listref Args - finds all products attached to this term and all terms below in the graph GO::Model::GeneProduct n_deep_products Usage - my $count = $term->n_deep_products; Returns - int Args - filter (hashref) - or string "recount" gets the count for the *dsitinct* number of GO::Model::GeneProduct entries annotated at OR BELOW this level. if you have set the filters in GO::AppHandle then these filters will be used in determining the count. Remember, if you did not explicitly set the filters, then the default filter will be used, which is [!IEA] (i.e. curated associations only, see www.geneontology.org for a discussion of evidence codes). Note: currently only the speciesdb filter is respected. It turns out to be very expensive to do the set arithmetic for distinct recursive gene counts with different evidence combinations. Because each product belongs to one speciesdb only, the speciesdb counts are mutually exclusive, which makes this easier. # get the number of gene products that have been annotated # as transcription factors in worm and fly discounting # uncurated automatic annotations $apph->filters({evcodes=>["!IEA"], speciesdbs=>["SGD", "FB"]}); $term = $apph->get_term({name=>"transcription factor"}); print $term->n_deep_products; The count will be cached, so if you alter the filter parameters be sure to get a recount like this: my $count = $term->n_deep_products("recount"); TODO: make the recount automatic if the filter is changed PERFORMANCE NOTE 1: When you ask the AppHandle to give you a list of GO::Model::Term objects, it may decide to populate this attribute when building the terms in a fast and efficient way. Therefore you should avoid setting the filters *after* you have created the objects otherwise it will have to refetch all these values slowing things down. PERFORMANCE NOTE 2: If you are using the SQL GO::AppHandle implementation, then this call will probably involve a query to the *gene_produc_count* table. If you populated the database you are using yourself, make sure this table is filled otherwise this will be an expensive query. GO::Model::GeneProduct n_products Usage - as n_deep_products Returns - Args - see docs for n_deep_products gets a count of products AT THIS LEVEL ONLY GO::Model::GeneProduct loadtime Title : loadtime Usage : Function: Example : Returns : time term was loaded into datasource Args : none perl v5.14.2 2013-02-07 GO::Model::Term(3pm)