Class | Bio::Genscan::Report::Exon |
In: |
lib/bio/appl/genscan/report.rb
|
Parent: | Object |
TYPES | = | { 'Init' => 'Initial exon', 'Intr' => 'Internal exon', 'Term' => 'Terminal exon', 'Sngl' => 'Single-exon gene', 'Prom' => 'Promoter', 'PlyA' => 'poly-A signal' |
score | -> | coding_region_score |
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. |
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 318 318: 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
Bio::Genescan::Report::Exon.parser
# 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
Bio::Genescan::Report::Exon#acceptor_score
"I/Ac" field.
# File lib/bio/appl/genscan/report.rb, line 355 355: def acceptor_score 356: @i_ac 357: end
Bio::Genescan::Report::Exon#donor_score
"Do/T" field.
# File lib/bio/appl/genscan/report.rb, line 364 364: def donor_score 365: @do_t 366: end
Bio::Genescan::Report::Exon#exon_type_long
Returns a human-readable "Type" of exon.
# File lib/bio/appl/genscan/report.rb, line 339 339: def exon_type_long 340: TYPES[exon_type] 341: end
Bio::Genescan::Report::Exon#range
Returns Range object of the region.
# File lib/bio/appl/genscan/report.rb, line 347 347: def range 348: Range.new(@first, @last) 349: end