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#!/usr/bin/env ruby
require 'helper'
require 'etc'
class Test2CRBBlast < Test::Unit::TestCase
context 'crb-blast' do
setup do
@blaster = CRB_Blast::CRB_Blast.new('test/query2.fasta', 'test/target2.fasta')
@dbs = @blaster.makedb
@run = @blaster.run_blast(1e-5, Etc.nprocessors, false)
@load = @blaster.load_outputs
@recips = @blaster.find_reciprocals
@secondaries = @blaster.find_secondaries
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 'setup2 should run ok' do
ans = @blaster != nil
assert_equal ans, true
end
should 'break input file into pieces' do
files = @blaster.split_input('test/query2.fasta', 4)
assert_equal 4, files.size
files.each do |file|
assert File.exist?(file)
end
# little teardown
files.each do |file|
File.delete(file)
end
end
should 'break input file into no more pieces than there are sequences' do
files = @blaster.split_input('test/query.fasta', 16)
assert_equal 11, files.size
files.each do |file|
assert File.exist?(file)
end
# little teardown
files.each do |file|
File.delete(file)
end
end
should 'run blast should check if the databases exist yet' do
tmp = CRB_Blast::CRB_Blast.new('test/query2.fasta',
'test/target2.fasta')
assert_equal false, tmp.run_blast(10,1,false)
end
should 'load output should check if the databases exist' do
tmp = CRB_Blast::CRB_Blast.new('test/query2.fasta',
'test/target2.fasta')
assert_raise RuntimeError do
tmp.load_outputs
end
end
should 'find reciprocals' do
assert_equal 7, @recips
end
should 'add secondary hits' do
assert_equal 2, @secondaries
end
should 'get non reciprocal hits' do
count=0
@blaster.missed.each_pair do |key, value|
value.each do |i|
count+=1
end
end
assert_equal count,70
end
end
end
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