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#!/usr/bin/env ruby
testdata_files = ["Arabidopsis-C99826.fna",
"Atinsert.fna",
"Duplicate.fna",
"Ecoli-section1.fna",
"Ecoli-section2.fna",
"example_1.fa",
"nowildcardatend.fna",
"nowildcardatend_rev.fna",
"rcr_testseq.fa",
"Reads1.fna",
"Reads2.fna",
"Reads3.fna",
"Repfind-example.fna",
"sain.fna",
"Scaffold_102.fa",
"Small.fna",
"Smalldup.fna",
"test1.fasta",
"trna_glutamine.fna"]
gttestdata_files = ["chntxx.fna",
"hs5hcmvcg.fna",
"humdystrop.fna",
"humghcsa.fna",
"humhbb.fna",
"humhdabcd.fna",
"humhprtb.fna",
"mipacga.fna",
"mpocpcg.fna",
"mpomtcg.fna",
"vaccg.fna",
"Wildcards.fna",
"ychrIII.fna"]
test_files = testdata_files.map {|f| "testdata/#{f}"}
if ENV.has_key?("GTTESTDATA")
grumbachpath = ENV["GTTESTDATA"] + "/DNA-mix/Grumbach.fna"
test_files += gttestdata_files.map {|f| "#{grumbachpath}/#{f}"}
end
test_files.each do |filename|
if not File.exists?(filename)
STDERR.puts "#{filename} does not exist"
exit 1
else
cmd = "scripts/cmp-seex.rb --seedlength 0 --silent --inputfile #{filename}"
puts "run #{cmd}"
if not system(cmd)
STDERR.puts "FAILURE: #{cmd}"
exit 1
end
end
end
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