Module: UniProt
- Extended by:
- Resource
- Defined in:
- lib/rbbt/sources/uniprot.rb
Constant Summary collapse
- UNIPROT_TEXT =
"http://www.uniprot.org/uniprot/[PROTEIN].txt"
- UNIPROT_FASTA =
"http://www.uniprot.org/uniprot/[PROTEIN].fasta"
Class Method Summary collapse
- .cath(protein) ⇒ Object
- .cath_domains(protein) ⇒ Object
- .features(protein) ⇒ Object
- .get_organism_ids(url, organism = nil) ⇒ Object
- .get_uniprot_entry(uniprotids) ⇒ Object
- .get_uniprot_sequence(uniprotids) ⇒ Object
- .pdbs(protein) ⇒ Object
- .pdbs_covering_aa_position(protein, aa_position) ⇒ Object
- .sequence(protein) ⇒ Object
- .variants(protein) ⇒ Object
Class Method Details
.cath(protein) ⇒ Object
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# File 'lib/rbbt/sources/uniprot.rb', line 276 def self.cath(protein) text = get_uniprot_entry(protein) cath = {} text.split(/\n/).each{|l| next unless l =~ /^DR\s+Gene3D; G3DSA:(.*)\./ id, description, cuantity = $1.split(";").collect{|v| v.strip} cath[id] = {:description => description, :cuantity => cuantity} } cath end |
.cath_domains(protein) ⇒ Object
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# File 'lib/rbbt/sources/uniprot.rb', line 288 def self.cath_domains(protein) pdbs = pdbs(protein).keys.uniq pdbs.collect do |pdb| Cath.domains_for_pdb(pdb) end.flatten.compact end |
.features(protein) ⇒ Object
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# File 'lib/rbbt/sources/uniprot.rb', line 188 def self.features(protein) text = get_uniprot_entry(protein) text = text.split(/\n/).select{|line| line =~ /^FT/} * "\n" parts = text.split(/^(FT \w+)/) parts.shift features = [] type = nil parts.each do |part| if part[0..1] == "FT" type = part.gsub(/FT\s+/,'') next end value = part.gsub("\nFT", '').gsub(/\s+/, ' ') case when value.match(/(\d+) (\d+) (.*)/) start, eend, description = $1, $2, $3 description.gsub(/^FT\s+/m, '') when value.match(/^\s+(\d+) (\d+)/) start, eend = $1, $2 description = nil else Log.debug "Value not understood: #{ value }" end feature = { :type => type, :start => start.to_i, :end => eend.to_i, :description => description, } features << feature end features end |
.get_organism_ids(url, organism = nil) ⇒ Object
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# File 'lib/rbbt/sources/uniprot.rb', line 12 def self.get_organism_ids(url, organism = nil) tsv = {} fields = [] TSV.traverse url, :type => :array, :bar => "Extracting UniProt IDs #{organism}" do |line| uni, type, value = line.split("\t") fields << type unless fields.include?(type) pos = fields.index type values = tsv[uni] values = [] if values.nil? values[pos] ||= [] values[pos] << value tsv[uni] = values end fields = fields.collect do |field| case field when "Gene_Name" "Associated Gene Name" when "Ensembl" "Ensembl Gene ID" when "Ensembl_TRS" "Ensembl Transcript ID" when "Ensembl_PRO" "Ensembl Protein ID" else field end end new = TSV.setup({}, :key_field => "UniProt/SwissProt Accession", :fields => fields, :type => :double, :namespace => organism) num_fields = fields.length tsv.each do |k,values| new_values = [nil] * num_fields new_values = values num_fields.times do |i| new_values[i] = [] if new_values[i].nil? end new[k] = new_values end new end |
.get_uniprot_entry(uniprotids) ⇒ Object
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# File 'lib/rbbt/sources/uniprot.rb', line 95 def self.get_uniprot_entry(uniprotids) _array = Array === uniprotids uniprotids = [uniprotids] unless Array === uniprotids uniprotids = uniprotids.compact.collect{|id| id} result_files = FileCache.cache_online_elements(uniprotids, 'uniprot-{ID}.xml') do |ids| result = {} ids.each do |id| begin Misc.try3times do content = Open.read(UNIPROT_TEXT.sub("[PROTEIN]", id), :wget_options => {:quiet => true}, :nocache => true) result[id] = content end rescue Log.error $!. end end result end uniprots = {} uniprotids.each{|id| uniprots[id] = Open.read(result_files[id]) } if _array uniprots else uniprots.values.first end end |
.get_uniprot_sequence(uniprotids) ⇒ Object
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# File 'lib/rbbt/sources/uniprot.rb', line 128 def self.get_uniprot_sequence(uniprotids) _array = Array === uniprotids uniprotids = [uniprotids] unless _array uniprotids = uniprotids.compact.collect{|id| id} result_files = FileCache.cache_online_elements(uniprotids, 'uniprot-sequence-{ID}') do |ids| result = {} ids.each do |id| begin Misc.try3times do url = UNIPROT_FASTA.sub "[PROTEIN]", id text = Open.read(url, :nocache => true) result[id] = text.split(/\n/).select{|line| line !~ /^>/} * "" end rescue Log.error $!. end end result end uniprots = {} uniprotids.each{|id| uniprots[id] = Open.read(result_files[id]) } if _array uniprots else uniprots.values.first end end |
.pdbs(protein) ⇒ Object
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# File 'lib/rbbt/sources/uniprot.rb', line 162 def self.pdbs(protein) text = get_uniprot_entry(protein) pdb = {} text.split(/\n/).each{|l| next unless l =~ /^DR\s+PDB; (.*)\./ id, method, resolution, region = $1.split(";").collect{|v| v.strip} begin chains, start, eend = region.match(/(\w+)=(\d+)-(\d+)/).values_at(1,2,3) start = start.to_i eend = eend.to_i start, eend = eend, start if start > eend rescue Log.warn("Error process Uniprot PDB line: #{l}") next end pdb[id.downcase] = {:method => method, :resolution => resolution, :region => (start..eend), :chains => chains} } pdb end |
.pdbs_covering_aa_position(protein, aa_position) ⇒ Object
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# File 'lib/rbbt/sources/uniprot.rb', line 295 def self.pdbs_covering_aa_position(protein, aa_position) UniProt.pdbs(protein).select do |pdb, info| info[:region].include? aa_position end end |
.sequence(protein) ⇒ Object
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# File 'lib/rbbt/sources/uniprot.rb', line 184 def self.sequence(protein) get_uniprot_sequence(protein) end |
.variants(protein) ⇒ Object
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# File 'lib/rbbt/sources/uniprot.rb', line 231 def self.variants(protein) text = get_uniprot_entry(protein) text = text.split(/\n/).select{|line| line =~ /^FT/} * "\n" parts = text.split(/^(FT \w+)/) parts.shift variants = [] type = nil parts.each do |part| if type.nil? type = part else if type !~ /VARIANT/ type = nil next end type = nil value = part.gsub("\nFT", '').gsub(/\s+/, ' ') # 291 291 K -> E (in sporadic cancers; somatic mutation). /FTId=VAR_045413. case when value.match(/(\d+) (\d+) ([A-Z])\s*\-\>\s*([A-Z]) (.*)\. \/FTId=(.*)/) start, eend, ref, mut, desc, id = $1, $2, $3, $4, $5, $6 when value.match(/(\d+) (\d+) (.*)\. \/FTId=(.*)/) start, eend, ref, mut, desc, id = $1, $2, nil, nil, $3, $4 else Log.debug "Value not understood: #{ value }" end variants << { :start => start, :end => eend, :ref => ref, :mut => mut, :desc => desc, :id => id, } end end variants end |