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
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
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