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#!/usr/bin/env ruby
require 'helper'
require 'etc'
class Test3CRBBlast < Test::Unit::TestCase
context 'crb-blast' do
setup do
end
teardown do
extensions = ["blast", "nsq", "nin", "nhr", "psq", "pin", "phr"]
Dir["*"].each do |file|
extensions.each do |extension|
if file =~ /.*\.#{extension}$/
File.delete(file)
end
end
end
end
should 'raise error when files don\'t exist' do
query = File.join(File.dirname(__FILE__), 'not_query.fasta')
target = File.join(File.dirname(__FILE__), 'not_target.fasta')
assert_raise IOError do
blaster = CRB_Blast::CRB_Blast.new(query, target)
end
end
should 'run' do
blaster = CRB_Blast::CRB_Blast.new('test/query.fasta',
'test/target.fasta')
blaster.run 1, 1, false
assert blaster.reciprocals
end
should 'work for query sequences with pipes' do
query = File.join(File.dirname(__FILE__), 'query3.fasta')
target = File.join(File.dirname(__FILE__), 'target.fasta')
blaster = CRB_Blast::CRB_Blast.new(query, target)
dbs = blaster.makedb
run = blaster.run_blast(1e-5, Etc.nprocessors, false)
load = blaster.load_outputs
recip_count = blaster.find_reciprocals
recips = blaster.reciprocals
assert_equal 3, recip_count, "reciprocal hits"
assert recips.has_key?("tr|C3Y8C9|C3Y8C9_BRAFL")
assert recips.has_key?("sp|O47426|ATP6_BRAFL")
assert recips.has_key?("sp|C4A0D9|BAP1_BRAFL")
end
end
end
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