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
317 def initialize(gnex, t, s, b, e, len, fr, ph, iac, dot, cr, prob, ts)
318   @gene_number, @number = gnex.split(".").map {|n| n.to_i }
319   @exon_type = t
320   @strand    = s
321   @first     = b.to_i
322   @last      = e.to_i
323   @length    = len.to_i
324   @frame     = fr
325   @phase     = ph
326   @i_ac      = iac.to_i
327   @do_t      = dot.to_i
328   @score     = cr.to_i
329   @p_value   = prob.to_f
330   @t_score   = ts.to_f
331 end
parser(line) click to toggle source

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

    # File lib/bio/appl/genscan/report.rb
266 def self.parser(line)
267   e = line.strip.split(/ +/)
268   case line
269   when /PlyA/, /Prom/
270     e[12] = e[6].clone
271     e[11] = 0
272     [6,7,8,9,10].each {|i| e[i] = nil }
273   end
274   self.new(e[0], e[1], e[2], e[3], e[4], e[5], e[6], 
275            e[7], e[8], e[9], e[10], e[11], e[12])
276 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
354 def acceptor_score
355   @i_ac
356 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
363 def donor_score
364   @do_t
365 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
338 def exon_type_long
339   TYPES[exon_type]
340 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
346 def range 
347   Range.new(@first, @last)
348 end
termination_score()
Alias for: donor_score