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#!/usr/bin/env ruby
require 'helper'
require 'etc'
class TestCRBBlast < Test::Unit::TestCase
context 'crb-blast' do
setup do
query = File.join(File.dirname(__FILE__), 'query.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
@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 'setup should run ok' do
ans = @blaster != nil
assert_equal ans, true
end
should 'determine that the target is a protein sequence' do
prot = @blaster.target_is_prot
assert_equal @dbs, ['query', 'target']
assert_equal prot, true
end
should 'run blast' do
assert_equal @run, true
end
should 'load outputs' do
assert_equal @load, [15,15]
end
should 'find reciprocals' do
assert_equal @recips, 10
end
should 'check if contig has reciprocal hit' do
assert_equal @blaster.has_reciprocal?("scaffold3"), true
end
should 'not find fake scaffold name' do
assert_equal @blaster.has_reciprocal?("not_a_scaffold"), false
end
should 'get query results' do
count=0
@blaster.query_results.each_pair do |key, list|
list.each do |hit|
count+=1
end
end
cmd = "wc -l query_into_target.1.blast"
lines = `#{cmd}`.to_i
assert_equal count, lines
end
should 'output all reciprocal hits' do
a = @blaster.reciprocals
assert_equal a["scaffold3"][0].target, "AT3G44735.1"
assert_equal a["scaffold5"][0].target, "AT5G13650.2"
end
should 'get number of reciprocals' do
assert_equal 10, @blaster.size
end
end
end
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