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comparison Flash_wrapper.rb @ 1:e70d522bcaae draft default tip

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author biowebdb
date Thu, 20 Mar 2014 14:58:18 -0400
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0:79fa20b1445f 1:e70d522bcaae
1 #!/usr/bin/ruby
2 require 'logger'
3 require "#{ENV['biowebdb']}/bioinformatics/Bioinformatics"
4 c = Bioinformatics.program 'Flash'
5 c.logger(Logger.new(STDOUT))
6 c.sequence1 = ARGV[0]
7 c.sequence2 = ARGV[1]
8 c.readLen = ARGV[2]
9 c.fragLen = ARGV[3]
10 c.maxOverlap = ARGV[4]
11 c.workPath = '/tmp/'
12 c.execute(c.lineCommand)
13
14 Kernel.system("cp #{c.outExtended} #{ARGV[5]}")
15 Kernel.system("cp #{c.outNotComb1} #{ARGV[6]}")
16 Kernel.system("cp #{c.outNotComb2} #{ARGV[7]}")
17