Module: UniProt

Extended by:
Resource
Defined in:
lib/rbbt/sources/uniprot.rb

Constant Summary collapse

UNIPROT_TEXT = 
"https://www.uniprot.org/uniprot/[PROTEIN].txt"
UNIPROT_FASTA = 
"https://www.uniprot.org/uniprot/[PROTEIN].fasta"

Class Method Summary collapse

Class Method Details

.cath(protein) ⇒ Object 



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# File 'lib/rbbt/sources/uniprot.rb', line 290

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 302

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 195

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(/(\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
    when value.match(/(\d+) (.*)/)
      start, description = $1, $2
      eend = start
      description.gsub(/^FT\s+/m, '')
    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"
    when "GeneID"
      "Entrez Gene 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 102

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 $!.message
      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 135

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 $!.message
      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 169

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 309

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 191

def self.sequence(protein)
  get_uniprot_sequence(protein)
end

.variants(protein) ⇒ Object 



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# File 'lib/rbbt/sources/uniprot.rb', line 245

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