Mercurial > repos > yufei-luo > s_mart

import unittest
import os
from commons.core.utils.FileUtils import FileUtils
from shutil import rmtree
from commons.launcher.LaunchPhyML import LaunchPhyML


class Test_F_LaunchPhyML(unittest.TestCase):

    def setUp(self):
        self._curTestDir = os.getcwd()
        self._testPrefix = 'test_LRA'
        try:
            os.makedirs(self._testPrefix)
        except:pass
        os.chdir(self._testPrefix)


        self._inputFastaFileName = "%s_input.fa" % self._testPrefix
        self._obsOutputFileName = self._inputFastaFileName +'_obs.phylip'
        self._expOutputFileName = "%s_exp.phylip" % self._testPrefix
        self._writeInputFile()

#    def tearDown(self):
#        os.chdir(self._curTestDir)
#        try:
#            rmtree(self._testPrefix)
#        except:pass

    def test_run(self):
        #phylip use only same length sequences
        self._writeExpFile()
        ilauncher = LaunchPhyML(self._inputFastaFileName,verbosity=7)
        ilauncher.run()
        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))


#    def test_run_as_script(self):
#        self._writeExpOutputFile_wo_refseq()
#        cmd = 'LaunchPhyML.py -i %s -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName)
#        os.system(cmd)
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))


    def _writeInputFile(self):
        InputFile = open(self._inputFastaFileName, 'w')
        InputFile.write(""">sequence1
GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC
GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT
GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAG
>sequence2
GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA
GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG
GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGG
>sequence3
ATCTTAGTTTTGCTGAGCGCCTTCATGGCTGCTTGACTATCAGACAGTATAGCAATGTCC
TTGCCATGATAGTTCCTTTTCAGATTAAACTCTGCACAGCGTCCAATAGCACAGACTTCA
GCTTGAATGCTGGTGTATCTGCCCATTGATTCGTGGTATTTCAACCTGGG
""")
        InputFile.close()

    def _writeExpFile(self):
        InputFile = open(self._expOutputFileName, 'w')
        InputFile.write(""" 3  170
sequence1      GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGG
sequence2      GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCG
sequence3      ATCTTAGTTTTGCTGAGCGCCTTCATGGCTGCTTGACTATCAGACAGTAT

CCCCGGGTTCGATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGG
TGATCCTGGAGACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAG
AGCAATGTCCTTGCCATGATAGTTCCTTTTCAGATTAAACTCTGCACAGC

AGTTTGCATGTTCTCCCTGTGCCTGCGTGGGTTCTCTCCGGGTACTCCGG
CCTGCTTCTCCCTCTGCCTGGGGCGGCACGGTGGTGTGGTGGTTAGCACT
GTCCAATAGCACAGACTTCAGCTTGAATGCTGGTGTATCTGCCCATTGAT

CTTCCTCCCACAGTCCAAAG
GTTGCCTCACAGCAAGAAGG
TCGTGGTATTTCAACCTGGG""")
        InputFile.close()

if __name__ == "__main__":
    unittest.main()
author	m-zytnicki
date	Mon, 29 Apr 2013 03:23:29 -0400
parents	94ab73e8a190
children