Class Bio::SPTR
In: lib/bio/db/embl/sptr.rb  (CVS)
Parent: EMBLDB

Parser class for UniProtKB/SwissProt and TrEMBL database entry.

Methods

aalen   aaseq   cc   cc_web_resource   dr   dt   entry   entry_id   entry_name   ft   gene_name   gene_names   gn   hi   id_line   molecule   molecule_type   oh   os   ox   protein_name   ref   references   seq   sequence_length   set_RN   sq   synonyms  

Included Modules

Bio::EMBLDB::Common

External Aliases

dr -> embl_dr
  Backup Bio::EMBLDB#dr as embl_dr

Public Instance methods

aalen()

Alias for sequence_length

aaseq()

Alias for seq

cc(topic = nil)

returns contents in the CC lines.

returns an object of contents in the TOPIC.

returns contents of the "ALTERNATIVE PRODUCTS".

  • Bio::SPTR#cc(‘ALTERNATIVE PRODUCTS’) -> Hash 
     {'Event' => str,
  'Named isoforms' => int,
  'Comment' => str,
  'Variants'=>[{'Name' => str, 'Synonyms' => str, 'IsoId' => str, 'Sequence' => []}]}

 CC   -!- ALTERNATIVE PRODUCTS:
 CC       Event=Alternative splicing; Named isoforms=15;
 ...
 CC         placentae isoforms. All tissues differentially splice exon 13;
 CC       Name=A; Synonyms=no del;
 CC         IsoId=P15529-1; Sequence=Displayed;

returns contents of the "DATABASE".

  • Bio::SPTR#cc(‘DATABASE’) -> Array 
     [{'NAME'=>str,'NOTE'=>str, 'WWW'=>URI,'FTP'=>URI}, ...]

 CC   -!- DATABASE: NAME=Text[; NOTE=Text][; WWW="Address"][; FTP="Address"].

returns contents of the "MASS SPECTROMETRY".

  • Bio::SPTR#cc(‘MASS SPECTROMETRY’) -> Array 
     [{'MW"=>float,'MW_ERR'=>float, 'METHOD'=>str,'RANGE'=>str}, ...]

 CC   -!- MASS SPECTROMETRY: MW=XXX[; MW_ERR=XX][; METHOD=XX][;RANGE=XX-XX].

CC lines (>=0, optional)

  CC   -!- TISSUE SPECIFICITY: HIGHEST LEVELS FOUND IN TESTIS. ALSO PRESENT
  CC       IN LIVER, KIDNEY, LUNG AND BRAIN.

  CC   -!- TOPIC: FIRST LINE OF A COMMENT BLOCK;
  CC       SECOND AND SUBSEQUENT LINES OF A COMMENT BLOCK.

See also www.expasy.org/sprot/userman.html#CC_line

[Source]

# File lib/bio/db/embl/sptr.rb, line 613
  def cc(topic = nil)
    unless @data['CC']
      cc  = Hash.new
      comment_border= '-' * (77 - 4 + 1)
      dlm = /-!- /

      # 12KD_MYCSM has no CC lines.
      return cc if get('CC').size == 0
      
      cc_raw = fetch('CC')

      # Removing the copyright statement.
      cc_raw.sub!(/ *---.+---/m, '')

      # Not any CC Lines without the copyright statement.
      return cc if cc_raw == ''

      begin
        cc_raw, copyright = cc_raw.split(/#{comment_border}/)[0]
        cc_raw = cc_raw.sub(dlm,'')
        cc_raw.split(dlm).each do |tmp|
          tmp = tmp.strip

          if /(^[A-Z ]+[A-Z]): (.+)/ =~ tmp
            key  = $1
            body = $2
            body.gsub!(/- (?!AND)/,'-')
            body.strip!
            unless cc[key]
              cc[key] = [body]
            else
              cc[key].push(body)
            end
          else
            raise ["Error: [#{entry_id}]: CC Lines", '"', tmp, '"',
                   '', get('CC'),''].join("\n")
          end
        end
      rescue NameError
        if fetch('CC') == ''
          return {}
        else
          raise ["Error: Invalid CC Lines: [#{entry_id}]: ",
                 "\n'#{self.get('CC')}'\n", "(#{$!})"].join
        end
      rescue NoMethodError
      end
      
      @data['CC'] = cc
    end


    case topic
    when 'ALLERGEN'
      return @data['CC'][topic]
    when 'ALTERNATIVE PRODUCTS'
      return cc_alternative_products(@data['CC'][topic])
    when 'BIOPHYSICOCHEMICAL PROPERTIES'
      return cc_biophysiochemical_properties(@data['CC'][topic])
    when 'BIOTECHNOLOGY'
      return @data['CC'][topic]
    when 'CATALITIC ACTIVITY'
      return cc_catalytic_activity(@data['CC'][topic])
    when 'CAUTION'
      return cc_caution(@data['CC'][topic])
    when 'COFACTOR'
      return @data['CC'][topic]
    when 'DEVELOPMENTAL STAGE'
      return @data['CC'][topic].to_s
    when 'DISEASE'
      return @data['CC'][topic].to_s
    when 'DOMAIN'
      return @data['CC'][topic]
    when 'ENZYME REGULATION'
      return @data['CC'][topic].to_s
    when 'FUNCTION'
      return @data['CC'][topic].to_s
    when 'INDUCTION'
      return @data['CC'][topic].to_s
    when 'INTERACTION'
      return cc_interaction(@data['CC'][topic])
    when 'MASS SPECTROMETRY'
      return cc_mass_spectrometry(@data['CC'][topic])
    when 'MISCELLANEOUS'
      return @data['CC'][topic]
    when 'PATHWAY'
      return cc_pathway(@data['CC'][topic])
    when 'PHARMACEUTICAL'
      return @data['CC'][topic]
    when 'POLYMORPHISM'
      return @data['CC'][topic]
    when 'PTM'
      return @data['CC'][topic]
    when 'RNA EDITING'
      return cc_rna_editing(@data['CC'][topic])
    when 'SIMILARITY'
      return @data['CC'][topic]
    when 'SUBCELLULAR LOCATION'
      return cc_subcellular_location(@data['CC'][topic])
    when 'SUBUNIT'
      return @data['CC'][topic]
    when 'TISSUE SPECIFICITY'
      return @data['CC'][topic]
    when 'TOXIC DOSE'
      return @data['CC'][topic]
    when 'WEB RESOURCE'
      return cc_web_resource(@data['CC'][topic])
    when 'DATABASE'
      # DATABASE: NAME=Text[; NOTE=Text][; WWW="Address"][; FTP="Address"].
      tmp = Array.new
      db = @data['CC']['DATABASE']
      return db unless db

      db.each do |e|
        db = {'NAME' => nil, 'NOTE' => nil, 'WWW' => nil, 'FTP' => nil}
        e.sub(/.$/,'').split(/;/).each do |line|
          case line
          when /NAME=(.+)/
            db['NAME'] = $1
          when /NOTE=(.+)/
            db['NOTE'] = $1
          when /WWW="(.+)"/
            db['WWW'] = $1
          when /FTP="(.+)"/
            db['FTP'] = $1
          end 
        end
        tmp.push(db)
      end
      return tmp
    when nil
      return @data['CC']
    else
      return @data['CC'][topic]
    end
  end
cc_web_resource(data)

CC -!- WEB RESOURCE: NAME=ResourceName[; NOTE=FreeText][; URL=WWWAddress].

[Source]

# File lib/bio/db/embl/sptr.rb, line 925
  def cc_web_resource(data)
    data.map {|x|
      entry = {'NAME' => nil, 'NOTE' => nil, 'URL' => nil}
      x.split(';').each do |y|
        case y
        when /NAME=(.+)/
          entry['NAME'] = $1.strip
        when /NOTE=(.+)/
          entry['NOTE'] = $1.strip
        when /URL="(.+)"/
          entry['URL'] = $1.strip
        end
      end
      entry
    }
  end
dr(key = nil)

Bio::SPTR#dr

[Source]

# File lib/bio/db/embl/sptr.rb, line 960
  def dr(key = nil)
    unless key
      embl_dr
    else
      embl_dr[key].map {|x|
        {'Accession' => x[0],
         'Version' => x[1],
         ' ' => x[2],
         'Molecular Type' => x[3]}
      }
    end
  end
dt(key = nil)

returns a Hash of information in the DT lines. 

 hash keys:
   ['created', 'sequence', 'annotation']
 also Symbols acceptable (ASAP):
   [:created, :sequence, :annotation]

returns a String of information in the DT lines by a given key..

DT Line; date (3/entry)

  DT DD-MMM-YYY (rel. NN, Created)
  DT DD-MMM-YYY (rel. NN, Last sequence update)
  DT DD-MMM-YYY (rel. NN, Last annotation update)

[Source]

# File lib/bio/db/embl/sptr.rb, line 123
  def dt(key = nil)
    return dt[key] if key
    return @data['DT'] if @data['DT']

    part = self.get('DT').split(/\n/)
    @data['DT'] = {
      'created'    => part[0].sub(/\w{2}   /,'').strip,
      'sequence'   => part[1].sub(/\w{2}   /,'').strip,
      'annotation' => part[2].sub(/\w{2}   /,'').strip
    }
  end
entry()

Alias for entry_id

entry_id()

returns a ENTRY_NAME in the ID line.

[Source]

# File lib/bio/db/embl/sptr.rb, line 79
  def entry_id
    id_line('ENTRY_NAME')
  end
entry_name()

Alias for entry_id

ft(feature_key = nil)

returns contents in the feature table.

Examples

 sp = Bio::SPTR.new(entry)
 ft = sp.ft
 ft.class #=> Hash
 ft.keys.each do |feature_key|
   ft[feature_key].each do |feature|
     feature['From'] #=> '1'
     feature['To']   #=> '21'
     feature['Description'] #=> ''
     feature['FTId'] #=> ''
     feature['diff'] #=> []
     feature['original'] #=> [feature_key, '1', '21', '', '']
   end
 end
  • Bio::SPTR#ft -> Hash 
     {FEATURE_KEY => [{'From' => int, 'To' => int,
                   'Description' => aStr, 'FTId' => aStr,
                   'diff' => [original_residues, changed_residues],
                   'original' => aAry }],...}

returns an Array of the information about the feature_name in the feature table.

FT Line; feature table data (>=0, optional)

  Col     Data item
  -----   -----------------
   1- 2   FT
   6-13   Feature name
  15-20   `FROM' endpoint
  22-27   `TO' endpoint
  35-75   Description (>=0 per key)
  -----   -----------------

Note: ‘FROM’ and ‘TO’ endopoints are allowed to use non-numerial charactors including ’<’, ’>’ or ’?’. (c.f. ’<1’, ’?42’)

See also www.expasy.org/sprot/userman.html#FT_line

[Source]

# File lib/bio/db/embl/sptr.rb, line 1025
  def ft(feature_key = nil)
    return ft[feature_key] if feature_key
    return @data['FT'] if @data['FT']

    table = []
    begin
      get('FT').split("\n").each do |line|
        if line =~ /^FT   \w/
          feature = line.chomp.ljust(74)
          table << [feature[ 5..12].strip,   # Feature Name
                    feature[14..19].strip,   # From
                    feature[21..26].strip,   # To
                    feature[34..74].strip ]  # Description
        else
          table.last << line.chomp.sub!(/^FT +/, '')
        end
      end

      # Joining Description lines
      table = table.map { |feature| 
        ftid = feature.pop if feature.last =~ /FTId=/
        if feature.size > 4
          feature = [feature[0], 
                     feature[1], 
                     feature[2], 
                     feature[3, feature.size - 3].join(" ")]
        end
        feature << if ftid then ftid else '' end
      }

      hash = {}
      table.each do |feature|
        hash[feature[0]] = [] unless hash[feature[0]]
        hash[feature[0]] << {
          # Removing '<', '>' or '?' in FROM/TO endopoint.
          'From' => feature[1].sub(/\D/, '').to_i,  
          'To'   => feature[2].sub(/\D/, '').to_i, 
          'Description' => feature[3], 
          'FTId' => feature[4].to_s.sub(/\/FTId=/, '').sub(/\.$/, ''),
          'diff' => [],
          'original' => feature
        }

        case feature[0]
        when 'VARSPLIC', 'VARIANT', 'VAR_SEQ', 'CONFLICT'
          case hash[feature[0]].last['Description']
          when /(\w[\w ]*\w*) - ?> (\w[\w ]*\w*)/
            original_res = $1
            changed_res = $2
            original_res = original_res.gsub(/ /,'').strip
            chenged_res = changed_res.gsub(/ /,'').strip
          when /Missing/i
            original_res = seq.subseq(hash[feature[0]].last['From'],
                                      hash[feature[0]].last['To'])
            changed_res = ''
          end
          hash[feature[0]].last['diff'] = [original_res, chenged_res]
        end
      end
    rescue
      raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n'#{self.get('FT')}'\n"
    end

    @data['FT'] = hash
  end
gene_name()

returns a String of the first gene name in the GN line.

[Source]

# File lib/bio/db/embl/sptr.rb, line 275
  def gene_name
    gene_names.first
  end
gene_names()

returns a Array of gene names in the GN line.

[Source]

# File lib/bio/db/embl/sptr.rb, line 264
  def gene_names
    gn # set @data['GN'] if it hasn't been already done
    if @data['GN'].first.class == Hash then
      @data['GN'].collect { |element| element[:name] }
    else
      @data['GN'].first
    end
  end
gn()

returns gene names in the GN line.

New UniProt/SwissProt format:

where <gene record> is: 

                   { :name => '...',
                     :synonyms => [ 's1', 's2', ... ],
                     :loci   => [ 'l1', 'l2', ... ],
                     :orfs     => [ 'o1', 'o2', ... ]
                   }

Old format:

GN Line: Gene name(s) (>=0, optional)

[Source]

# File lib/bio/db/embl/sptr.rb, line 188
  def gn
    unless @data['GN']
      case fetch('GN')
      when /Name=/,/ORFNames=/
        @data['GN'] = gn_uniprot_parser
      else
        @data['GN'] = gn_old_parser
      end
    end
    @data['GN']
  end
hi()

The HI line

Bio::SPTR#hi #=> hash

[Source]

# File lib/bio/db/embl/sptr.rb, line 529
  def hi
    unless @data['HI']
      @data['HI'] = []
      fetch('HI').split(/\. /).each do |hlist|
        hash = {'Category' => '',  'Keywords' => [], 'Keyword' => ''}
        hash['Category'], hash['Keywords'] = hlist.split(': ')
        hash['Keywords'] = hash['Keywords'].split('; ')
        hash['Keyword'] = hash['Keywords'].pop
        hash['Keyword'].sub!(/\.$/, '')
        @data['HI'] << hash
      end
    end
    @data['HI']
  end
id_line(key = nil)

returns a Hash of the ID line.

returns a content (Int or String) of the ID line by a given key. Hash keys: [‘ENTRY_NAME’, ‘DATA_CLASS’, ‘MODECULE_TYPE’, ‘SEQUENCE_LENGTH’]

ID Line

  ID   P53_HUMAN      STANDARD;      PRT;   393 AA.
  #"ID  #{ENTRY_NAME} #{DATA_CLASS}; #{MOLECULE_TYPE}; #{SEQUENCE_LENGTH}."

Examples

  obj.id_line  #=> {"ENTRY_NAME"=>"P53_HUMAN", "DATA_CLASS"=>"STANDARD",
                    "SEQUENCE_LENGTH"=>393, "MOLECULE_TYPE"=>"PRT"}

  obj.id_line('ENTRY_NAME') #=> "P53_HUMAN"

[Source]

# File lib/bio/db/embl/sptr.rb, line 63
  def id_line(key = nil)
    return id_line[key] if key
    return @data['ID'] if @data['ID']

    part = @orig['ID'].split(/ +/)         
    @data['ID'] = {
      'ENTRY_NAME'      => part[1],
      'DATA_CLASS'      => part[2].sub(/;/,''),
      'MOLECULE_TYPE'   => part[3].sub(/;/,''),
      'SEQUENCE_LENGTH' => part[4].to_i 
    }
  end
molecule()

returns a MOLECULE_TYPE in the ID line.

A short-cut for Bio::SPTR#id_line(‘MOLECULE_TYPE’).

[Source]

# File lib/bio/db/embl/sptr.rb, line 89
  def molecule
    id_line('MOLECULE_TYPE')
  end
molecule_type()

Alias for molecule

oh()

The OH Line;

OH NCBI_TaxID=TaxID; HostName. br.expasy.org/sprot/userman.html#OH_line

[Source]

# File lib/bio/db/embl/sptr.rb, line 358
  def oh
    unless @data['OH']
      @data['OH'] = fetch('OH').split("\. ").map {|x|
        if x =~ /NCBI_TaxID=(\d+);/
          taxid = $1
        else
          raise ArgumentError, ["Error: Invalid OH line format (#{self.entry_id}):",
                                $!, "\n", get('OH'), "\n"].join
          
        end
        if x =~ /NCBI_TaxID=\d+; (.+)/ 
          host_name = $1
          host_name.sub!(/\.$/, '')
        else
          host_name = nil
        end
        {'NCBI_TaxID' => taxid, 'HostName' => host_name}
      }
    end
    @data['OH']
  end
os(num = nil)

returns a Array of Hashs or a String of the OS line when a key given.

  • Bio::EMBLDB#os -> Array 
 [{'name' => '(Human)', 'os' => 'Homo sapiens'},
  {'name' => '(Rat)', 'os' => 'Rattus norveticus'}]
  • Bio::EPTR#os[0] -> Hash 
 {'name' => "(Human)", 'os' => 'Homo sapiens'}
  • Bio::SPTR#os[0][‘name’] -> "(Human)"
  • Bio::EPTR#os(0) -> "Homo sapiens (Human)"

OS Line; organism species (>=1)

 OS   Genus species (name).
 OS   Genus species (name0) (name1).
 OS   Genus species (name0) (name1).
 OS   Genus species (name0), G s0 (name0), and G s (name0) (name1).
 OS   Homo sapiens (Human), and Rarrus norveticus (Rat)
 OS   Hippotis sp. Clark and Watts 825.
 OS   unknown cyperaceous sp.

[Source]

# File lib/bio/db/embl/sptr.rb, line 297
  def os(num = nil)
    unless @data['OS']
      os = Array.new
      fetch('OS').split(/, and|, /).each do |tmp|
        if tmp =~ /(\w+ *[\w\d \:\'\+\-\.]+[\w\d\.])/
          org = $1
          tmp =~ /(\(.+\))/ 
          os.push({'name' => $1, 'os' => org})
        else
          raise "Error: OS Line. #{$!}\n#{fetch('OS')}\n"
        end
      end
      @data['OS'] = os
    end

    if num
      # EX. "Trifolium repens (white clover)"
      return "#{@data['OS'][num]['os']} #{@data['OS'][num]['name']}"
    else
      return @data['OS']
    end
  end
ox()

returns a Hash of oraganism taxonomy cross-references.

OX Line; organism taxonomy cross-reference (>=1 per entry)

 OX   NCBI_TaxID=1234;
 OX   NCBI_TaxID=1234, 2345, 3456, 4567;

[Source]

# File lib/bio/db/embl/sptr.rb, line 341
  def ox
    unless @data['OX']
      tmp = fetch('OX').sub(/\.$/,'').split(/;/).map { |e| e.strip }
      hsh = Hash.new
      tmp.each do |e|
        db,refs = e.split(/=/)
        hsh[db] = refs.split(/, */)
      end
      @data['OX'] = hsh
    end
    return @data['OX']
  end
protein_name()

returns the proposed official name of the protein.

DE Line; description (>=1)

 "DE #{OFFICIAL_NAME} (#{SYNONYM})"
 "DE #{OFFICIAL_NAME} (#{SYNONYM}) [CONTEINS: #1; #2]."
 OFFICIAL_NAME  1/entry
 SYNONYM        >=0
 CONTEINS       >=0

[Source]

# File lib/bio/db/embl/sptr.rb, line 144
  def protein_name
    name = ""
    if de_line = fetch('DE') then
      str = de_line[/^[^\[]*/] # everything preceding the first [ (the "contains" part)
      name = str[/^[^(]*/].strip
      name << ' (Fragment)' if str =~ /fragment/i
    end
    return name
  end
ref()

returns contents in the R lines.

  • Bio::EMBLDB::Common#ref -> [ <refernece information Hash>* ]

where <reference information Hash> is: 

 {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '',
  'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}

R Lines

  • RN RC RP RX RA RT RL RG

[Source]

# File lib/bio/db/embl/sptr.rb, line 394
  def ref
    unless @data['R']
      @data['R'] = [get('R').split(/\nRN   /)].flatten.map { |str|
        hash = {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '', 
               'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}
        str = 'RN   ' + str unless /^RN   / =~ str

        str.split("\n").each do |line|
          if /^(R[NPXARLCTG])   (.+)/ =~ line
            hash[$1] += $2 + ' '
          else
            raise "Invalid format in R lines, \n[#{line}]\n"
          end
        end

        hash['RN'] = set_RN(hash['RN'])
        hash['RC'] = set_RC(hash['RC'])
        hash['RP'] = set_RP(hash['RP'])
        hash['RX'] = set_RX(hash['RX'])
        hash['RA'] = set_RA(hash['RA'])
        hash['RT'] = set_RT(hash['RT'])
        hash['RL'] = set_RL(hash['RL'])
        hash['RG'] = set_RG(hash['RG'])

        hash
      }

    end
    @data['R']
  end
references()

returns Bio::Reference object from Bio::EMBLDB::Common#ref.

[Source]

# File lib/bio/db/embl/sptr.rb, line 488
  def references
    unless @data['references']
      ary = self.ref.map {|ent|
        hash = Hash.new('')
        ent.each {|key, value|
          case key
          when 'RA'
            hash['authors'] = value.split(/, /)
          when 'RT'
            hash['title'] = value
          when 'RL'
            if value =~ /(.*) (\d+) \((\d+)\), (\d+-\d+) \((\d+)\)$/
              hash['journal'] = $1
              hash['volume']  = $2
              hash['issue']   = $3
              hash['pages']   = $4
              hash['year']    = $5
            else
              hash['journal'] = value
            end
          when 'RX'  # PUBMED, MEDLINE
            value.split('.').each {|item|
              tag, xref = item.split(/; /).map {|i| i.strip }
              hash[ tag.downcase ]  = xref
            }
          end
        }
        Reference.new(hash)
      }
      @data['references'] = References.new(ary)
    end
    @data['references']
  end
seq()

returns a Bio::Sequence::AA of the amino acid sequence.

blank Line; sequence data (>=1)

[Source]

# File lib/bio/db/embl/sptr.rb, line 1135
  def seq
    unless @data['']
      @data[''] = Sequence::AA.new( fetch('').gsub(/ |\d+/,'') )
    end
    return @data['']
  end
sequence_length()

returns a SEQUENCE_LENGTH in the ID line.

A short-cut for Bio::SPTR#id_line(‘SEQUENCE_LENGHT’).

[Source]

# File lib/bio/db/embl/sptr.rb, line 98
  def sequence_length
    id_line('SEQUENCE_LENGTH')
  end
set_RN(data)

[Source]

# File lib/bio/db/embl/sptr.rb, line 425
  def set_RN(data)
    data.strip
  end
sq(key = nil)

returns a Hash of conteins in the SQ lines.

  • Bio::SPTRL#sq -> hsh

returns a value of a key given in the SQ lines.

  • Bio::SPTRL#sq(key) -> int or str
  • Keys: [‘MW’, ‘mw’, ‘molecular’, ‘weight’, ‘aalen’, ‘len’, ‘length’, 
           'CRC64']

SQ Line; sequence header (1/entry)

   SQ   SEQUENCE   233 AA;  25630 MW;  146A1B48A1475C86 CRC64;
   SQ   SEQUENCE  \d+ AA; \d+ MW;  [0-9A-Z]+ CRC64;

MW, Dalton unit. CRC64 (64-bit Cyclic Redundancy Check, ISO 3309).

[Source]

# File lib/bio/db/embl/sptr.rb, line 1107
  def sq(key = nil)
    unless @data['SQ']
      if fetch('SQ') =~ /(\d+) AA\; (\d+) MW; (.+) CRC64;/
        @data['SQ'] = { 'aalen' => $1.to_i, 'MW' => $2.to_i, 'CRC64' => $3 }
      else
        raise "Invalid SQ Line: \n'#{fetch('SQ')}'"
      end
    end

    if key
      case key
      when /mw/, /molecular/, /weight/
        @data['SQ']['MW']
      when /len/, /length/, /AA/
        @data['SQ']['aalen']
      else
        @data['SQ'][key]
      end
    else 
      @data['SQ']
    end
  end
synonyms()

returns an array of synonyms (unofficial names).

synonyms are each placed in () following the official name on the DE line.

[Source]

# File lib/bio/db/embl/sptr.rb, line 158
  def synonyms
    ary = Array.new
    if de_line = fetch('DE') then
      line = de_line.sub(/\[.*\]/,'') # ignore stuff between [ and ].  That's the "contains" part
      line.scan(/\([^)]+/) do |synonym| 
        unless synonym =~ /fragment/i then 
          ary << synonym[1..-1].strip # index to remove the leading (  
        end
      end
    end
    return ary
  end

[Validate]