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
Source
# 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
Bio::Genescan::Report::Exon.new(gene_number, exon_type, strand, first, end, length, frame, phase, acceptor_score, donor_score, score, p_value, t_score)
Source
# 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
Bio::Genescan::Report::Exon.parser
Public Instance Methods
Source
# File lib/bio/appl/genscan/report.rb 354 def acceptor_score 355 @i_ac 356 end
Bio::Genescan::Report::Exon#acceptor_score
“I/Ac” field.
Source
# File lib/bio/appl/genscan/report.rb 363 def donor_score 364 @do_t 365 end
Bio::Genescan::Report::Exon#donor_score
“Do/T” field.
Source
# File lib/bio/appl/genscan/report.rb 338 def exon_type_long 339 TYPES[exon_type] 340 end
Bio::Genescan::Report::Exon#exon_type_long
Returns a human-readable “Type” of exon.
Source
# File lib/bio/appl/genscan/report.rb 346 def range 347 Range.new(@first, @last) 348 end
Bio::Genescan::Report::Exon#range
Returns Range object of the region.