Class: Bio::Fasta::Report::Hit

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/fasta/format10.rb

Defined Under Namespace

Classes: Query, Target

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(data) ⇒ Hit

Returns a new instance of Hit.



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# File 'lib/bio/appl/fasta/format10.rb', line 111

def initialize(data)
  score, query, target = data.split(/\n>/)

  @definition, *score = score.split(/\n/)
  @score = {}

  pat = /;\s+([^:]+):\s+(.*)/

  score.each do |x|
    if pat.match(x)
      @score[$1] = $2
    end
  end

  @query = Query.new(query)
  @target = Target.new(target)
end

Instance Attribute Details

#definition ⇒ Object (readonly)

Returns the value of attribute definition.



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# File 'lib/bio/appl/fasta/format10.rb', line 128

def definition
  @definition
end

#query ⇒ Object (readonly)

Returns the value of attribute query.



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# File 'lib/bio/appl/fasta/format10.rb', line 128

def query
  @query
end

#score ⇒ Object (readonly)

Returns the value of attribute score.



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# File 'lib/bio/appl/fasta/format10.rb', line 128

def score
  @score
end

#target ⇒ Object (readonly)

Returns the value of attribute target.



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# File 'lib/bio/appl/fasta/format10.rb', line 128

def target
  @target
end

Instance Method Details

#bit_score ⇒ Object

Bit score



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# File 'lib/bio/appl/fasta/format10.rb', line 144

def bit_score
  if @score['fa_bits']
    @score['fa_bits'].to_f
  elsif @score['sw_bits']
    @score['sw_bits'].to_f
  elsif @score['fx_bits']
    @score['fx_bits'].to_f
  elsif @score['tx_bits']
    @score['tx_bits'].to_f
  end
end

#direction ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 156

def direction
  @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame']
end

#evalue ⇒ Object

E-value score



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# File 'lib/bio/appl/fasta/format10.rb', line 131

def evalue
  if @score['fa_expect']
    @score['fa_expect'].to_f
  elsif @score['sw_expect']
    @score['sw_expect'].to_f
  elsif @score['fx_expect']
    @score['fx_expect'].to_f
  elsif @score['tx_expect']
    @score['tx_expect'].to_f
  end
end

#identity ⇒ Object

percent identity



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# File 'lib/bio/appl/fasta/format10.rb', line 166

def identity
  @score['sw_ident'].to_f
end

#lap_at ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 237

def lap_at
  [ query_start, query_end, target_start, target_end ]
end

#overlap ⇒ Object

overlap length



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# File 'lib/bio/appl/fasta/format10.rb', line 171

def overlap
  @score['sw_overlap'].to_i
end

#query_def ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 185

def query_def
  @query.definition
end

#query_end ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 225

def query_end
  @query.stop
end

#query_id ⇒ Object

Shortcuts for the methods of Bio::Fasta::Report::Hit::Query



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# File 'lib/bio/appl/fasta/format10.rb', line 177

def query_id
  @query.entry_id
end

#query_len ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 193

def query_len
  @query.length
end

#query_seq ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 203

def query_seq
  @query.sequence
end

#query_start ⇒ Object

Information on matching region



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# File 'lib/bio/appl/fasta/format10.rb', line 221

def query_start
  @query.start
end

#query_type ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 211

def query_type
  @query.moltype
end

#sw ⇒ Object

Smith-Waterman score



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# File 'lib/bio/appl/fasta/format10.rb', line 161

def sw
  @score['sw_score'].to_i
end

#target_def ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 189

def target_def
  @target.definition
end

#target_end ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 233

def target_end
  @target.stop
end

#target_id ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 181

def target_id
  @target.entry_id
end

#target_len ⇒ Object

Shortcuts for the methods of Bio::Fasta::Report::Hit::Target



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# File 'lib/bio/appl/fasta/format10.rb', line 199

def target_len
  @target.length
end

#target_seq ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 207

def target_seq
  @target.sequence
end

#target_start ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 229

def target_start
  @target.start
end

#target_type ⇒ Object 



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# File 'lib/bio/appl/fasta/format10.rb', line 215

def target_type
  @target.moltype
end