class Bio::Genscan::Report::Exon
Container class of a predicted gene structure.¶ ↑
Constants
- TYPES
Attributes
Returns “CodRg” field.
Returns “Type” field.
Returns Returns first position of the region. “Begin” field.
Returns “Fr” field.
Returns
Returns Returns last position of the region. “End” field.
Returns “Ex”, exon number field
Returns “P” field.
Returns “Ph” field.
Returns “CodRg” field.
Returns “S” field.
Returns “Tscr” field.
Public Class Methods
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 318 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
Bio::Genescan::Report::Exon.parser
# File lib/bio/appl/genscan/report.rb, line 267 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
Bio::Genescan::Report::Exon#acceptor_score
“I/Ac” field.
# File lib/bio/appl/genscan/report.rb, line 355 def acceptor_score @i_ac end
Bio::Genescan::Report::Exon#donor_score
“Do/T” field.
# File lib/bio/appl/genscan/report.rb, line 364 def donor_score @do_t end
Bio::Genescan::Report::Exon#exon_type_long
Returns a human-readable “Type” of exon.
# File lib/bio/appl/genscan/report.rb, line 339 def exon_type_long TYPES[exon_type] end
Bio::Genescan::Report::Exon#range
Returns Range object of the region.
# File lib/bio/appl/genscan/report.rb, line 347 def range Range.new(@first, @last) end