Class: Bio::DAS

Inherits:
Object show all
Defined in:
lib/bio/io/das.rb,
lib/bio/shell/plugin/das.rb

Defined Under Namespace

Classes: DNA, DSN, ENTRY_POINT, FEATURE, GFF, GROUP, LINK, SEGMENT, SEQUENCE, TARGET, TYPE, TYPES

Instance Method Summary collapse

Constructor Details

#initialize(url = 'http://www.wormbase.org:80/db/') ⇒ DAS

Specify DAS server to connect



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# File 'lib/bio/io/das.rb', line 31

def initialize(url = 'http://www.wormbase.org:80/db/')
  @server = url.chomp('/')
end

Instance Method Details

#dna(dsn, entry_point, start, stop) ⇒ Object 



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# File 'lib/bio/io/das.rb', line 35

def dna(dsn, entry_point, start, stop)
  seg = Bio::DAS::SEGMENT.region(entry_point, start, stop)
  self.get_dna(dsn, seg).first.sequence
end

#features(dsn, entry_point, start, stop) ⇒ Object 



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# File 'lib/bio/io/das.rb', line 40

def features(dsn, entry_point, start, stop)
  seg = Bio::DAS::SEGMENT.region(entry_point, start, stop)
  self.get_features(dsn, seg)
end

#get_dna(dsn, segments) ⇒ Object

Returns an Array of Bio::DAS::DNA. The ‘dsn’ can be a String or a Bio::DAS::DSN object. The ‘segments’ can be a Bio::DAS::SEGMENT object or an Array of Bio::DAS::SEGMENT



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# File 'lib/bio/io/das.rb', line 103

def get_dna(dsn, segments)
  ary = []

  dsn = dsn.source if dsn.instance_of?(DSN)
  segments = [segments] if segments.instance_of?(SEGMENT)

  opts = []
  segments.each do |s|
    opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
  end

  result = Bio::Command.post_form("#{@server}/das/#{dsn}/dna", opts)
  doc = REXML::Document.new(result.body)
  doc.elements.each('/descendant::SEQUENCE') do |e|
    sequence = DNA.new
    sequence.entry_id = e.attributes['id']
    sequence.start = e.attributes['start']
    sequence.stop = e.attributes['stop']
    sequence.version = e.attributes['version']
    e.elements.each do |el|
      sequence.sequence = Bio::Sequence::NA.new(el.text)
      sequence.length = el.attributes['length'].to_i
    end
    ary << sequence
  end
  ary
end

#get_dsn ⇒ Object

Returns an Array of Bio::DAS::DSN



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# File 'lib/bio/io/das.rb', line 47

def get_dsn
  ary = []
  result = Bio::Command.post_form("#{@server}/das/dsn")
  doc = REXML::Document.new(result.body)
  doc.elements.each('/descendant::DSN') do |ee|
    dsn = DSN.new
    ee.elements.each do |e|
      case e.name
      when 'SOURCE'
        dsn.source = e.text
        dsn.source_id = e.attributes['id']
        dsn.source_version = e.attributes['version']
      when 'MAPMASTER'
        dsn.mapmaster = e.text
      when 'DESCRIPTION'
        dsn.description = e.text
        dsn.description_href = e.attributes['href']
      end
    end
    ary << dsn
  end
  ary
end

#get_entry_points(dsn) ⇒ Object

Returns Bio::DAS::ENTRY_POINT. The ‘dsn’ can be a String or a Bio::DAS::DSN object.



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# File 'lib/bio/io/das.rb', line 73

def get_entry_points(dsn)
  entry_point = ENTRY_POINT.new
  if dsn.instance_of?(Bio::DAS::DSN)
    src = dsn.source 
  else
    src = dsn
  end
  result = Bio::Command.post_form("#{@server}/das/#{src}/entry_points")
  doc = REXML::Document.new(result.body)
  doc.elements.each('/descendant::ENTRY_POINTS') do |ee|
    entry_point.href = ee.attributes['href']
    entry_point.version = ee.attributes['version']
    ee.elements.each do |e|
      segment = SEGMENT.new
      segment.entry_id = e.attributes['id']
      segment.start = e.attributes['start']
      segment.stop = e.attributes['stop'] || e.attributes['size']
      segment.orientation = e.attributes['orientation']
      segment.subparts = e.attributes['subparts']
      segment.description = e.text
      entry_point.segments << segment
    end
  end
  entry_point
end

#get_features(dsn, segments = [], categorize = false, feature_ids = [], group_ids = []) ⇒ Object

Returns a Bio::DAS::GFF object. The ‘dsn’ can be a String or a Bio::DAS::DSN object. The ‘segments’ is optional and can be a Bio::DAS::SEGMENT object or an Array of Bio::DAS::SEGMENT



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# File 'lib/bio/io/das.rb', line 213

def get_features(dsn, segments = [], categorize = false, feature_ids = [], group_ids = [])
  # arguments 'type' and 'category' are deprecated
  gff = GFF.new

  dsn = dsn.source if dsn.instance_of?(DSN)
  segments = [segments] if segments.instance_of?(SEGMENT)

  opts = []
  segments.each do |s|
    opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
  end
  if categorize
    opts << "categorize=yes"	# default is 'no'
  end
  feature_ids.each do |fid|
    opts << "feature_id=#{fid}"
  end
  group_ids.each do |gid|
    opts << "group_id=#{gid}"
  end

  result = Bio::Command.post_form("#{@server}/das/#{dsn}/features", opts)
  doc = REXML::Document.new(result.body)
  doc.elements.each('/descendant::GFF') do |elem|
    gff.version = elem.attributes['version']
    gff.href = elem.attributes['href']
    elem.elements.each('SEGMENT') do |ele|
      segment = SEGMENT.new
      segment.entry_id = ele.attributes['id']
      segment.start = ele.attributes['start']
      segment.stop = ele.attributes['stop']
      segment.version = ele.attributes['version']
      segment.label = ele.attributes['label']
      ele.elements.each do |el|
        feature = FEATURE.new
        feature.entry_id = el.attributes['id']
        feature.label = el.attributes['label']
        el.elements.each do |e|
          case e.name
          when 'TYPE'
            type = TYPE.new
            type.entry_id = e.attributes['id']
            type.category = e.attributes['category']
            type.reference = e.attributes['referrence']
            type.label = e.text
            feature.types << type
          when 'METHOD'
            feature.method_id = e.attributes['id']
            feature.method = e.text
          when 'START'
            feature.start = e.text
          when 'STOP', 'END'
            feature.stop = e.text
          when 'SCORE'
            feature.score = e.text
          when 'ORIENTATION'
            feature.orientation = e.text
          when 'PHASE'
            feature.phase = e.text
          when 'NOTE'
            feature.notes << e.text
          when 'LINK'
            link = LINK.new
            link.href = e.attributes['href']
            link.text = e.text
            feature.links << link
          when 'TARGET'
            target = TARGET.new
            target.entry_id = e.attributes['id']
            target.start = e.attributes['start']
            target.stop = e.attributes['stop']
            target.name = e.text
            feature.targets << target
          when 'GROUP'
            group = GROUP.new
            group.entry_id = e.attributes['id']
            group.label = e.attributes['label']
            group.type = e.attributes['type']
            e.elements.each do |ee|
              case ee.name
              when 'NOTE'		# in GROUP
                group.notes << ee.text
              when 'LINK'		# in GROUP
                link = LINK.new
                link.href = ee.attributes['href']
                link.text = ee.text
                group.links << link
              when 'TARGET'		# in GROUP
                target = TARGET.new
                target.entry_id = ee.attributes['id']
                target.start = ee.attributes['start']
                target.stop = ee.attributes['stop']
                target.name = ee.text
                group.targets << target
              end
            end
            feature.groups << group
          end
        end
        segment.features << feature
      end
      gff.segments << segment
    end
  end
  gff
end

#get_sequence(dsn, segments) ⇒ Object

Returns an Array of Bio::DAS::SEQUENCE. The ‘dsn’ can be a String or a Bio::DAS::DSN object. The ‘segments’ can be a Bio::DAS::SEGMENT object or an Array of Bio::DAS::SEGMENT



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# File 'lib/bio/io/das.rb', line 135

def get_sequence(dsn, segments)
  ary = []

  dsn = dsn.source if dsn.instance_of?(DSN)
  segments = [segments] if segments.instance_of?(SEGMENT)

  opts = []
  segments.each do |s|
    opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
  end

  result = Bio::Command.post_form("#{@server}/das/#{dsn}/sequence", opts)
  doc = REXML::Document.new(result.body)
  doc.elements.each('/descendant::SEQUENCE') do |e|
    sequence = SEQUENCE.new
    sequence.entry_id = e.attributes['id']
    sequence.start = e.attributes['start']
    sequence.stop = e.attributes['stop']
    sequence.moltype = e.attributes['moltype']
    sequence.version = e.attributes['version']
    case sequence.moltype
    when /dna|rna/i		# 'DNA', 'ssRNA', 'dsRNA'
      sequence.sequence = Bio::Sequence::NA.new(e.text)
    when /protein/i		# 'Protein
      sequence.sequence = Bio::Sequence::AA.new(e.text)
    else
      sequence.sequence = e.text
    end
    ary << sequence
  end
  ary
end

#get_types(dsn, segments = []) ⇒ Object

Returns a Bio::DAS::TYPES object. The ‘dsn’ can be a String or a Bio::DAS::DSN object. The ‘segments’ is optional and can be a Bio::DAS::SEGMENT object or an Array of Bio::DAS::SEGMENT



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# File 'lib/bio/io/das.rb', line 172

def get_types(dsn, segments = [])	# argument 'type' is deprecated
  types = TYPES.new

  dsn = dsn.source if dsn.instance_of?(DSN)
  segments = [segments] if segments.instance_of?(SEGMENT)

  opts = []
  segments.each do |s|
    opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
  end

  result = Bio::Command.post_form("#{@server}/das/#{dsn}/types", opts)
  doc = REXML::Document.new(result.body)
  doc.elements.each('/descendant::GFF') do |ee|
    types.version = ee.attributes['version']
    types.href = ee.attributes['href']
    ee.elements.each do |e|
      segment = SEGMENT.new
      segment.entry_id = e.attributes['id']
      segment.start = e.attributes['start']
      segment.stop = e.attributes['stop']
      segment.version = e.attributes['version']
      segment.label = e.attributes['label']
      e.elements.each do |el|
        t = TYPE.new
        t.entry_id = el.attributes['id']
        t.method = el.attributes['method']
        t.category = el.attributes['category']
        t.count = el.text.to_i
        segment.types << t
      end
      types.segments << segment
    end
  end
  types
end

#list_sequences ⇒ Object 



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# File 'lib/bio/shell/plugin/das.rb', line 14

def list_sequences
  result = ""
  self.get_dsn.each do |dsn|
    src = dsn.source_id
    self.get_entry_points(src).each do |ep|
      data = [src, ep.entry_id, ep.start.to_i, ep.stop.to_i, "# #{ep.description}"].join("\t") + "\n"
      puts data
      result += data
    end
  end
  return result
end