Class: Bio::Blat::StreamedReport

Inherits:
Report
  • Object
show all
Defined in:
lib/bio-blat-tools/blat-tools.rb

Class Method Summary collapse

Class Method Details

.each_best_hit(text = '') ⇒ Object 



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# File 'lib/bio-blat-tools/blat-tools.rb', line 31

def self.each_best_hit(text = '')

	best_aln = Hash.new
	self.each_hit(text) do |hit|
		current_matches = hit.match 
		current_name = hit.query_id
		current_identity = hit.percent_identity
		current_score = hit.score
		best_aln[current_name] = hit if best_aln[current_name] == nil or current_score > best_aln[current_name] .score
	end
	best_aln.each_value { |val| yield  val }
end

.each_hit(text = '') ⇒ Object 



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# File 'lib/bio-blat-tools/blat-tools.rb', line 7

def self.each_hit(text = '')
				flag = false
				head = []

				text.each_line do |line|
					if flag then
						yield Hit.new(line)
					else

			if /^\d/ =~ line then # for headerless data
				flag = true
				redo
			end
			line = line.chomp
			if /\A\-+\s*\z/ =~ line
				flag = true
			else
				head << line
			end
		end
	end
end