class Bio::Blat
Public Class Methods
align(database , query , output) { |hit| ... }
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# File lib/bio/BIOExtensions.rb, line 4 def self.align(database , query , output) cmdline = "blat #{database} #{query} #{output}" puts $stderr.puts cmdline status, stdout, stderr = systemu cmdline if status.exitstatus == 0 alns = Array.new unless block_given? blat_aln = Bio::Blat::Report.new(Bio::FlatFile.open(output).to_io) #p blat_aln blat_aln.each_hit() do |hit| if block_given? yield hit else alns << hit end end return alns unless block_given? else raise Exception.new(), "Error running exonerate. Command line was '#{cmdline}'\nBlat STDERR was:\n#{stderr}" end end