Class Bio::Genscan::Report::Exon
In: lib/bio/appl/genscan/report.rb
Parent: Object

Container class of a predicted gene structure.

Methods

acceptor_score   donor_score   exon_type_long   initiation_score   new   parser   range   termination_score  

Constants

TYPES = { 'Init' => 'Initial exon', 'Intr' => 'Internal exon', 'Term' => 'Terminal exon', 'Sngl' => 'Single-exon gene', 'Prom' => 'Promoter', 'PlyA' => 'poly-A signal'  

External Aliases

score -> coding_region_score

Attributes

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)

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

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

[Source]

     # File lib/bio/appl/genscan/report.rb, line 267
267:       def self.parser(line)
268:         e = line.strip.split(/ +/)
269:         case line
270:         when /PlyA/, /Prom/
271:           e[12] = e[6].clone
272:           e[11] = 0
273:           [6,7,8,9,10].each {|i| e[i] = nil }
274:         end
275:         self.new(e[0], e[1], e[2], e[3], e[4], e[5], e[6], 
276:                  e[7], e[8], e[9], e[10], e[11], e[12])
277:       end

Public Instance methods

acceptor_score()

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

"I/Ac" field.

[Source]

     # File lib/bio/appl/genscan/report.rb, line 355
355:       def acceptor_score
356:         @i_ac
357:       end
donor_score()

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

"Do/T" field.

[Source]

     # File lib/bio/appl/genscan/report.rb, line 364
364:       def donor_score
365:         @do_t
366:       end
exon_type_long()

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

Returns a human-readable "Type" of exon.

[Source]

     # File lib/bio/appl/genscan/report.rb, line 339
339:       def exon_type_long
340:         TYPES[exon_type]
341:       end
initiation_score()

Alias for acceptor_score

range()

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

Returns Range object of the region.

[Source]

     # File lib/bio/appl/genscan/report.rb, line 347
347:       def range 
348:         Range.new(@first, @last)
349:       end
termination_score()

Alias for donor_score

[Validate]