Module: Organism
- Extended by:
- Resource
- Defined in:
- lib/rbbt/sources/organism.rb
Defined Under Namespace
Classes: OrganismNotProcessedError
Constant Summary collapse
- ARCHIVE_MONTH_INDEX =
{}
Class Method Summary collapse
- .allowed_biomart_archives ⇒ Object
- .attach_translations(org, tsv, target = nil, fields = nil, options = {}) ⇒ Object
- .chromosome_sizes(organism = Organism.default_code("Hsa")) ⇒ Object
- .compare_archives(a1, a2) ⇒ Object
- .default_code(organism = "Hsa") ⇒ Object
- .entrez_taxid_organism(taxid) ⇒ Object
- .gene_list_bases(genes, organism = nil) ⇒ Object
- .gene_list_exon_bases(genes, organism = nil) ⇒ Object
- .guess_id(org, values) ⇒ Object
- .hg_build(organism) ⇒ Object
- .installable_organisms ⇒ Object
- .installed_organisms ⇒ Object
- .known_ids(name) ⇒ Object
- .liftOver(positions, source, target) ⇒ Object
- .normalize(org, list, target = nil, fields = nil, options = {}) ⇒ Object
- .organism(name) ⇒ Object
- .organism_code(name) ⇒ Object
- .organism_codes(organism = nil) ⇒ Object
- .organisms ⇒ Object
- .scientific_name(organism) ⇒ Object
Class Method Details
.allowed_biomart_archives ⇒ Object
52 53 54 55 56 |
# File 'lib/rbbt/sources/organism.rb', line 52 def self.allowed_biomart_archives Rbbt.etc.allowed_biomart_archives.exists? ? Rbbt.etc.allowed_biomart_archives.list : nil end |
.attach_translations(org, tsv, target = nil, fields = nil, options = {}) ⇒ Object
128 129 130 131 132 133 134 135 136 137 138 |
# File 'lib/rbbt/sources/organism.rb', line 128 def self.attach_translations(org, tsv, target = nil, fields = nil, = {}) Log.high "Attaching Translations for #{ org.inspect }, target #{target.inspect}, fields #{fields.inspect}" = Misc.add_defaults , :persist => true, :case_insensitive => false .merge! :key_field => target unless target.nil? .merge! :fields => fields unless fields.nil? index = identifiers(org).tsv tsv.attach index, :fields => [:key], :persist_input => true end |
.chromosome_sizes(organism = Organism.default_code("Hsa")) ⇒ Object
263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 |
# File 'lib/rbbt/sources/organism.rb', line 263 def self.chromosome_sizes(organism = Organism.default_code("Hsa")) chromosome_sizes = {} Organism[organism].glob_all("chromosome_*").each do |file| chromosome = file.split("_").last.split(".").first size = if Open.gzip?(file) || Open.bgzip?(file) CMD.cmd("zcat '#{ file }' | wc -c ").read else File.size(file) end chromosome_sizes[chromosome] = size.to_i end chromosome_sizes end |
.compare_archives(a1, a2) ⇒ Object
11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 |
# File 'lib/rbbt/sources/organism.rb', line 11 def self.compare_archives(a1, a2) a1 = a1.partition("/").last if a1 and a1.include? "/" a2 = a2.partition("/").last if a2 and a2.include? "/" return 0 if a1 == a2 return -1 if a1 and a2.nil? return 1 if a1.nil? and a2 m1,y1 = a1.match(/(...)(\d+)/).values_at 1, 2 m2,y2 = a2.match(/(...)(\d+)/).values_at 1, 2 y1 = y1.to_f y2 = y2.to_f ycmp = y1 <=> y2 return ycmp unless ycmp == 0 ARCHIVE_MONTH_INDEX[m1] <=> ARCHIVE_MONTH_INDEX[m2] end |
.default_code(organism = "Hsa") ⇒ Object
30 31 32 |
# File 'lib/rbbt/sources/organism.rb', line 30 def self.default_code(organism = "Hsa") organism.split("/").first << "/feb2014" end |
.entrez_taxid_organism(taxid) ⇒ Object
203 204 205 206 207 208 209 210 211 |
# File 'lib/rbbt/sources/organism.rb', line 203 def self.entrez_taxid_organism(taxid) all_organisms = Organism.installable_organisms all_organisms.each do |organism| return organism if Organism.entrez_taxids(organism).read.split("\n").include? taxid.to_s end raise "No organism identified for taxid #{taxid}. Supported organism are: #{all_organisms * ", "}" end |
.gene_list_bases(genes, organism = nil) ⇒ Object
213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 |
# File 'lib/rbbt/sources/organism.rb', line 213 def self.gene_list_bases(genes, organism = nil) if genes.respond_to? :orgnanism organism = genes.organism if organism.nil? genes = genes.clean_annotations end organism ||= "Hsa" @@gene_start_end ||= {} gene_start_end = @@gene_start_end[organism] ||= Organism.gene_positions(organism).tsv(:persist => true, :key_field => "Ensembl Gene ID", :fields => ["Gene Start", "Gene End"], :type => :list, :cast => :to_i, :unmamed => true) ranges = genes.collect{|gene| start, eend = gene_start_end[gene] if start.nil? or eend.nil? Log.low "Gene #{ gene } does not have range" next end (start..eend) }.compact Misc.total_length(ranges) end |
.gene_list_exon_bases(genes, organism = nil) ⇒ Object
235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 |
# File 'lib/rbbt/sources/organism.rb', line 235 def self.gene_list_exon_bases(genes, organism = nil) if genes.respond_to? :orgnanism organism = genes.organism if organism.nil? genes = genes.clean_annotations end organism ||= "Hsa" @@gene_exons_tsv ||= {} gene_exons = @@gene_exons_tsv[organism] ||= Organism.exons(organism).tsv(:persist => true, :key_field => "Ensembl Gene ID", :fields => ["Ensembl Exon ID"], :type => :flat, :merge => true, :unnamed => true) @@exon_range_tsv ||= {} exon_ranges = @@exon_range_tsv[organism] ||= Organism.exons(organism).tsv(:persist => true, :fields => ["Exon Chr Start", "Exon Chr End"], :type => :list, :cast => :to_i, :unnamed => true) exons = gene_exons.values_at(*genes).compact.flatten.uniq exon_ranges = exons.collect{|exon| if not exon_ranges.include? exon Log.low "Exon #{ exon } does not have range" next end pos = exon_ranges[exon] (pos.first..pos.last) }.compact Misc.total_length(exon_ranges) end |
.guess_id(org, values) ⇒ Object
166 167 168 169 170 171 172 173 174 175 176 177 |
# File 'lib/rbbt/sources/organism.rb', line 166 def self.guess_id(org, values) field_matches = TSV.field_match_counts(Organism.identifiers(org).produce, values) best = nil best_count = 0 field_matches.each do |field,count| if count > best_count best = field best_count = count end end [best, best_count] end |
.hg_build(organism) ⇒ Object
66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 |
# File 'lib/rbbt/sources/organism.rb', line 66 def self.hg_build(organism) require 'rbbt/sources/ensembl_ftp' raise "Only organism 'Hsa' (Homo sapiens) supported" unless organism =~ /^Hsa/ return 'hg20' unless organism =~ /\// date = organism.split("/")[1] release = Ensembl.releases[date] release_number = release.sub(/.*-/,'').to_i if release_number <= 54 'hg18' elsif release_number <= 75 'hg19' else 'hg38' end end |
.installable_organisms ⇒ Object
48 49 50 |
# File 'lib/rbbt/sources/organism.rb', line 48 def self.installable_organisms self.installed_organisms end |
.installed_organisms ⇒ Object
44 45 46 |
# File 'lib/rbbt/sources/organism.rb', line 44 def self.installed_organisms Rbbt.share.install.Organism.find.glob('???').collect{|f| File.basename(f)} end |
.known_ids(name) ⇒ Object
199 200 201 |
# File 'lib/rbbt/sources/organism.rb', line 199 def self.known_ids(name) TSV::Parser.new(Organism.identifiers(name).open).all_fields end |
.liftOver(positions, source, target) ⇒ Object
86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 |
# File 'lib/rbbt/sources/organism.rb', line 86 def self.liftOver(positions, source, target) source_hg = hg_build(source) target_hg = hg_build(target) map_url = "http://hgdownload.cse.ucsc.edu/goldenPath/#{source_hg}/liftOver/#{source_hg}To#{target_hg.sub('h', 'H')}.over.chain.gz" positions_bed = positions.collect{|position| chr, pos = position.split(":").values_at(0,1) ["chr" << chr, pos.to_i-1, pos, position] * "\t" } * "\n" + "\n" new_positions = {} TmpFile.with_file(positions_bed) do |source_bed| TmpFile.with_file() do |unmapped_file| TmpFile.with_file() do |map_file| Open.write(map_file, Open.read(map_url)) new_mutations = TmpFile.with_file() do |target_bed| FileUtils.chmod(755, Rbbt.software.opt.bin.liftOver.produce.find) CMD.cmd("#{Rbbt.software.opt.bin.liftOver.find} '#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'").read Open.read(target_bed) do |line| chr, position_alt, position, name = line.chomp.split("\t") chr.sub! /chr/, '' old_chr, old_position, *rest = name.split(":") new_positions[name] = ([chr, position].concat rest) * ":" end end end end end positions.collect do |position| new_positions[position] end end |
.normalize(org, list, target = nil, fields = nil, options = {}) ⇒ Object
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 |
# File 'lib/rbbt/sources/organism.rb', line 140 def self.normalize(org, list, target = nil, fields = nil, = {}) return [] if list.nil? or list.empty? = Misc.add_defaults , :persist => true, :case_insensitive => true, :double => false double = Misc. , :double .merge! :target => target unless target.nil? .merge! :fields => fields unless fields.nil? index = identifiers(org).index if Array === list if double index.values_at *list else index.values_at(*list).collect{|e| Misc.first e} end else if double index[list] else index[list].first end end end |
.organism(name) ⇒ Object
187 188 189 190 191 |
# File 'lib/rbbt/sources/organism.rb', line 187 def self.organism(name) installable_organisms.select{|organism| organism == name or Organism.scientific_name(organism) =~ /#{ name }/i }.first end |
.organism_code(name) ⇒ Object
193 194 195 196 197 |
# File 'lib/rbbt/sources/organism.rb', line 193 def self.organism_code(name) organisms.select{|organism| organism == name or Organism.scientific_name(organism) =~ /#{ name }/i }.first end |
.organism_codes(organism = nil) ⇒ Object
34 35 36 37 38 39 40 41 42 |
# File 'lib/rbbt/sources/organism.rb', line 34 def self.organism_codes(organism = nil) if organism Rbbt.etc.allowed_biomart_archives.list.collect{|build| [organism, build] * "/" } else Rbbt.etc.organisms.list.collect{|organism| organism =~ /\// ? organism : Rbbt.etc.allowed_biomart_archives.list.collect{|build| [organism, build] * "/" } + [organism] }.flatten.compact.uniq end end |
.organisms ⇒ Object
179 180 181 |
# File 'lib/rbbt/sources/organism.rb', line 179 def self.organisms Dir.glob(File.join(Organism.root.find, '*')).collect{|f| File.basename(f)} end |
.scientific_name(organism) ⇒ Object
183 184 185 |
# File 'lib/rbbt/sources/organism.rb', line 183 def self.scientific_name(organism) Organism[organism]["scientific_name"].produce.read.strip end |