class Bio::Genscan::Report::Exon

Container class of a predicted gene structure.

Constants

TYPES

Attributes

coding_region_score[R]

Returns “CodRg” field.

exon_type[R]

Returns “Type” field.

first[R]

Returns Returns first position of the region. “Begin” field.

frame[R]

Returns “Fr” field.

gene_number[R]

Returns

last[R]

Returns Returns last position of the region. “End” field.

number[R]

Returns “Ex”, exon number field

p_value[R]

Returns “P” field.

phase[R]

Returns “Ph” field.

score[R]

Returns “CodRg” field.

strand[R]

Returns “S” field.

t_score[R]

Returns “Tscr” field.

Public Class Methods

new(gnex, t, s, b, e, len, fr, ph, iac, dot, cr, prob, ts) click to toggle source

Bio::Genescan::Report::Exon.new(gene_number, #exon_type, strand, first, end, length, frame, phase, #acceptor_score, #donor_score, score, #p_value, #t_score)

# File lib/bio/appl/genscan/report.rb, line 317
def initialize(gnex, t, s, b, e, len, fr, ph, iac, dot, cr, prob, ts)
  @gene_number, @number = gnex.split(".").map {|n| n.to_i }
  @exon_type = t
  @strand    = s
  @first     = b.to_i
  @last      = e.to_i
  @length    = len.to_i
  @frame     = fr
  @phase     = ph
  @i_ac      = iac.to_i
  @do_t      = dot.to_i
  @score     = cr.to_i
  @p_value   = prob.to_f
  @t_score   = ts.to_f
end
parser(line) click to toggle source

Bio::Genescan::Report::Exon.parser

# File lib/bio/appl/genscan/report.rb, line 266
def self.parser(line)
  e = line.strip.split(/ +/)
  case line
  when /PlyA/, /Prom/
    e[12] = e[6].clone
    e[11] = 0
    [6,7,8,9,10].each {|i| e[i] = nil }
  end
  self.new(e[0], e[1], e[2], e[3], e[4], e[5], e[6], 
           e[7], e[8], e[9], e[10], e[11], e[12])
end

Public Instance Methods

acceptor_score() click to toggle source

Bio::Genescan::Report::Exon#acceptor_score

“I/Ac” field.

# File lib/bio/appl/genscan/report.rb, line 354
def acceptor_score
  @i_ac
end
Also aliased as: initiation_score
donor_score() click to toggle source

Bio::Genescan::Report::Exon#donor_score

“Do/T” field.

# File lib/bio/appl/genscan/report.rb, line 363
def donor_score
  @do_t
end
Also aliased as: termination_score
exon_type_long() click to toggle source

Bio::Genescan::Report::Exon#exon_type_long

Returns a human-readable “Type” of exon.

# File lib/bio/appl/genscan/report.rb, line 338
def exon_type_long
  TYPES[exon_type]
end
initiation_score()
Alias for: acceptor_score
range() click to toggle source

Bio::Genescan::Report::Exon#range

Returns Range object of the region.

# File lib/bio/appl/genscan/report.rb, line 346
def range 
  Range.new(@first, @last)
end
termination_score()
Alias for: donor_score