Class | Bio::Fasta::Report |
In: |
lib/bio/appl/fasta/format10.rb
|
Parent: | Object |
hits | [R] | Returns an Array of Bio::Fasta::Report::Hit objects. |
list | [R] | Returns the ‘The best scores are’ lines as a String. |
log | [R] | Returns the trailing lines including library size, execution date, fasta function used, and fasta versions as a String. |
program | [R] | Returns a Bio::Fasta::Report::Program object. |
# File lib/bio/appl/fasta/format10.rb, line 18 18: def initialize(data) 19: # header lines - brief list of the hits 20: if data.sub!(/.*\nThe best scores are/m, '') 21: data.sub!(/(.*)\n\n>>>/m, '') 22: @list = "The best scores are" + $1 23: else 24: data.sub!(/.*\n!!\s+/m, '') 25: data.sub!(/.*/) { |x| @list = x; '' } 26: end 27: 28: # body lines - fasta execution result 29: program, *hits = data.split(/\n>>/) 30: 31: # trailing lines - log messages of the execution 32: @log = hits.pop 33: @log.sub!(/.*<\n/m, '') 34: @log.strip! 35: 36: # parse results 37: @program = Program.new(program) 38: @hits = [] 39: 40: hits.each do |x| 41: @hits.push(Hit.new(x)) 42: end 43: end
Iterates on each Bio::Fasta::Report::Hit object.
# File lib/bio/appl/fasta/format10.rb, line 59 59: def each 60: @hits.each do |x| 61: yield x 62: end 63: end
Returns an Array of Bio::Fasta::Report::Hit objects having longer overlap length than ‘length_min’.
# File lib/bio/appl/fasta/format10.rb, line 77 77: def lap_over(length_min = 0) 78: list = [] 79: @hits.each do |x| 80: list.push(x) if x.overlap > length_min 81: end 82: return list 83: end
Returns an Array of Bio::Fasta::Report::Hit objects having better evalue than ‘evalue_max’.
# File lib/bio/appl/fasta/format10.rb, line 67 67: def threshold(evalue_max = 0.1) 68: list = [] 69: @hits.each do |x| 70: list.push(x) if x.evalue < evalue_max 71: end 72: return list 73: end