Module: GO
- Defined in:
- lib/rbbt/sources/go.rb
Overview
This module holds helper methods to deal with the Gene Ontology files. Right now all it does is provide a translation form id to the actual names.
Constant Summary collapse
- MULTIPLE_VALUE_FIELDS =
%w(is_a)
- TSV_GENE_ONTOLOGY =
File.join(Persist.cachedir, 'gene_ontology')
Class Method Summary collapse
- .ancestors_in(term, valid) ⇒ Object
- .goterms ⇒ Object
- .group_genes(list, valid = nil) ⇒ Object
- .id2ancestors(id) ⇒ Object
- .id2ancestors_by_type(id, type = 'is_a') ⇒ Object
- .id2name(id) ⇒ Object
- .id2namespace(id) ⇒ Object
- .info ⇒ Object
-
.init ⇒ Object
This method needs to be called before any translations can be made, it is called automatically the first time the id2name method is called.
Class Method Details
.ancestors_in(term, valid) ⇒ Object
96 97 98 99 100 101 102 103 104 105 |
# File 'lib/rbbt/sources/go.rb', line 96 def self.ancestors_in(term, valid) ancestors = id2ancestors(term) return ancestors if FalseClass === valid valid_ancestors = ancestors & valid return valid_ancestors if valid_ancestors.any? ancestors.inject([]) do |acc,ancestor| valid_a = ancestors_in ancestor, valid acc = acc + valid_a end.uniq end |
.goterms ⇒ Object
47 48 49 |
# File 'lib/rbbt/sources/go.rb', line 47 def self.goterms info.keys end |
.group_genes(list, valid = nil) ⇒ Object
107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 |
# File 'lib/rbbt/sources/go.rb', line 107 def self.group_genes(list, valid = nil) valid = %w(GO:0005886 GO:0005634 GO:0005730 GO:0005829) if valid.nil? compartment_leaves = {} list.zip(list.go_cc_terms).each do |gene,terms| terms = [] if terms.nil? valid_terms = terms & valid valid_terms = terms.collect{|term| (valid.include?(term) ? term : ancestors_in(term, valid)) }.flatten #valid_terms - GOTerm.setup(valid_terms).flat_ancestry.flatten valid_terms.each do |term| compartment_leaves[term] ||= [] compartment_leaves[term].push(gene) end end groups = {} while compartment_leaves.length > 1 # Group common group = false new_compartment_leaves = {} compartment_leaves.each do |c,l| if l.length > 1 groups[c] = l group = true new_compartment_leaves[c] = [c] else new_compartment_leaves[c] = l end end compartment_leaves = new_compartment_leaves # Pull-up leaves if group == false new_compartment_leaves = {} final = compartment_leaves.keys compartment_leaves compartment_leaves.each do |c,l| final = final - GOTerm.setup(c.dup).flat_ancestry end compartment_leaves.each do |c,l| if final.include? c valid_an = ancestors_in c, valid valid_an.each do |ancestor| new_compartment_leaves[ancestor] ||= [] new_compartment_leaves[ancestor].push(c) groups[ancestor].push(c) if groups[ancestor] end else new_compartment_leaves[c] = l end end compartment_leaves = new_compartment_leaves end end ng = {} groups.keys.reverse.each do |k| ng[k] = {items: groups[k].uniq, id: k, name: id2name(k)} end ng end |
.id2ancestors(id) ⇒ Object
82 83 84 |
# File 'lib/rbbt/sources/go.rb', line 82 def self.id2ancestors(id) id2ancestors_by_type(id, 'is_a') + id2ancestors_by_type(id, 'relationship') end |
.id2ancestors_by_type(id, type = 'is_a') ⇒ Object
60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 |
# File 'lib/rbbt/sources/go.rb', line 60 def self.id2ancestors_by_type(id, type='is_a') if id.kind_of? Array info.values_at(*id). select{|i| ! i[type].nil?}. collect{|i| res = i[type] res = [res] unless Array === res res.collect{|id| id.match(/(GO:\d+)/)[1] if id.match(/(GO:\d+)/) }.compact } else return [] if id.nil? or info[id].nil? or info[id][type].nil? res = info[id][type] res = [res] unless Array === res res. collect{|id| id.match(/(GO:\d+)/)[1] if id.match(/(GO:\d+)/) }.compact end end |
.id2name(id) ⇒ Object
51 52 53 54 55 56 57 58 |
# File 'lib/rbbt/sources/go.rb', line 51 def self.id2name(id) if id.kind_of? Array info.values_at(*id).collect{|i| i['name'] if i} else return nil if info[id].nil? info[id]['name'] end end |
.id2namespace(id) ⇒ Object
86 87 88 89 90 91 92 93 94 |
# File 'lib/rbbt/sources/go.rb', line 86 def self.id2namespace(id) self.init unless info if id.kind_of? Array info.values_at(*id).collect{|i| i['namespace'] if i} else return nil if info[id].nil? info[id]['namespace'] end end |
.info ⇒ Object
43 44 45 |
# File 'lib/rbbt/sources/go.rb', line 43 def self.info @@info ||= self.init end |
.init ⇒ Object
This method needs to be called before any translations can be made, it is called automatically the first time the id2name method is called. It loads the gene_ontology.obo file and extracts all the fields, although right now, only the name field is used.
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 |
# File 'lib/rbbt/sources/go.rb', line 19 def self.init Persist.persist_tsv(nil, 'gene_ontology', {}, :persist => true) do |info| info.serializer = :marshal if info.respond_to? :serializer Rbbt.share.databases.GO.gene_ontology.read.split(/\[Term\]/).each{|term| term_info = {} term.split(/\n/). select{|l| l =~ /:/}.each{|l| key, value = l.chomp.match(/(.*?):(.*)/).values_at(1,2) if MULTIPLE_VALUE_FIELDS.include? key.strip term_info[key.strip] ||= [] term_info[key.strip] << value.strip else term_info[key.strip] = value.strip end } next if term_info["id"].nil? info[term_info["id"]] = term_info } info end.tap{|o| o.unnamed = true} end |