#!/usr/bin/env python

#Copyright (C) 2009-2011 by Benedict Paten (benedictpaten@gmail.com)
#
#Released under the MIT license, see LICENSE.txt
import unittest
import sys

from cactus.shared.test import parseCactusSuiteTestOptions
from sonLib.bioio import TestStatus

from cactus.shared.test import getCactusInputs_random
from cactusTools.shared.test import runWorkflow_multipleExamples

class TestCase(unittest.TestCase):
    def testCactus_RandomAlignmentsOnly(self):
        """Build mafs from cactusDisks containing no trees, faces or reference.
        """
        runWorkflow_multipleExamples(getCactusInputs_random, #Just for the alignments.
                                     testNumber=TestStatus.getTestSetup(), 
                                     makeMAFs=True,buildTrees=False,buildFaces=False, buildReference=False)
    
    def testCactus_Random(self):
        """Build mafs from cactusDisks containing trees, face and an reference (the output will include the MAFS ordered by reference)
        """
        runWorkflow_multipleExamples(getCactusInputs_random, 
                                     testNumber=TestStatus.getTestSetup(), 
                                     makeMAFs=True)
        
def main():
    parseCactusSuiteTestOptions()
    sys.argv = sys.argv[:1]
    unittest.main()
        
if __name__ == '__main__':
    main()