view commons/tools/tests/Test_F_GetMultiAlignAndPhylogenyPerTErefSeq.py @ 18:94ab73e8a190

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import subprocess
import unittest
import os
from commons.core.utils.FileUtils import FileUtils
from commons.core.sql.DbMySql import DbMySql
from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq
from shutil import rmtree
from glob import glob

class Test_F_GetMultAlignAndPhylogenyPerTErefSeq(unittest.TestCase):
    
    def setUp(self):
        self._verbosity = 3
        
        self._testPrefix = 'Test_GMAAPperTErefSeq_'
        self._configFileName = "%sConfig.cfg" % self._testPrefix
        self._iDb = DbMySql()

        self.inPathTableName = "%sDmelChr4_chr_allTEs_nr_noSSR_join_path" % (self._testPrefix)
        self.inPathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
        self._iDb.createTable(self.inPathTableName, "path", self.inPathFileName, True)
        
        self.RefTETableName = "%sDmelChr4_refTEs" % (self._testPrefix)
        self.RefTEFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
        self._iDb.createTable(self.RefTETableName, "seq", self.RefTEFileName, True)
        
        self.genomeTableName = "%sDmelChr4_chr" % (self._testPrefix)
        self.genomeFileName = "%s/Tools/DmelChr4.fa" % os.environ["REPET_DATA"]
        self._iDb.createTable(self.genomeTableName, "seq", self.genomeFileName, True)

        try:
            os.makedirs(self._testPrefix)
        except:pass
        os.chdir(self._testPrefix)
        self._writeConfigFile()
        
#        self._expFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.txt" % os.environ["REPET_DATA"]
#        self._expFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.txt" % os.environ["REPET_DATA"]
#        self._expFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.txt" % os.environ["REPET_DATA"]
#        self._expFastaFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.fa" % os.environ["REPET_DATA"]
#        self._expFastaFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.fa" % os.environ["REPET_DATA"]
#        self._expFastaFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.fa" % os.environ["REPET_DATA"]

        
#        inputFastaFileName = "input_TEannot_refTEs.fa"
#        os.symlink(self._expFastaFileName_Copy, inputFastaFileName)
        
#        self._tableName = "Dummy_Atha_refTEs_seq"
#        self._iDb.createTable(self._tableName, "seq", inputFastaFileName, True)
#        os.remove(inputFastaFileName)      
#        
#        self._obsFileName_FullLengthCopy = "%s_FullLengthCopy.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
#        self._obsFileName_Copy = "%s_OneCopyAndMore.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
#        self._obsFileName_FullLengthFrag = "%s_FullLengthFrag.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
#        self._obsFastaFileName_FullLengthCopy = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthCopy)[0]
#        self._obsFastaFileName_Copy = "%s.fa" % os.path.splitext(self._obsFileName_Copy)[0]
#        self._obsFastaFileName_FullLengthFrag = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthFrag)[0]
        
    def tearDown(self):
#        self._iDb.dropTable(self.inPathTableName)
#        self._iDb.dropTable(self.RefTETableName)
#        self._iDb.dropTable(self.genomeTableName)
#        self._iDb.close()
        
        os.chdir("..")
#        try:
#            rmtree(self._testPrefix)
#        except:pass
        

#    def test_run_step1(self):
#        iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, configFileName=self._configFileName, step=1, verbosity=self._verbosity)
#        iGMAAPperTErefSeq.run()
#        
#        copiesFiles = glob("*_copies.fa")
#        self.assertTrue(len(copiesFiles) > 0)
#        self.assertTrue(os.stat("DmelChr4-B-R9-Map3_NoCat_copies.fa")[6] != 0)#check if file is empty
#    
#    def test_run_step1Step2Map(self):
#        iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="Map", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
#        iGMAAPperTErefSeq.run()
#        iGMAAPperTErefSeq.step = 2
#        iGMAAPperTErefSeq.run()
#
#        self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
#
#    def test_run_step1Step2RefAlign(self):
#        iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="RefAlign", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
#        iGMAAPperTErefSeq.run()
#        iGMAAPperTErefSeq.step = 2
#        iGMAAPperTErefSeq.run()
#
#        self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_refalign.fa_aln")[6] != 0)

    def test_run_step1Step2Step3Map(self):
        iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="Map", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
        iGMAAPperTErefSeq.run()
        iGMAAPperTErefSeq.step = 2
        iGMAAPperTErefSeq.run()
        iGMAAPperTErefSeq.step = 3
        iGMAAPperTErefSeq.run()

        self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
    
    def _writeConfigFile(self):
        f = open(self._configFileName, "w")
        f.write("[repet_env]\n")
        f.write("repet_host: %s\n" % os.environ["REPET_HOST"])
        f.write("repet_user: %s\n" % os.environ["REPET_USER"])
        f.write("repet_pw: %s\n" % os.environ["REPET_PW"])
        f.write("repet_db: %s\n" % os.environ["REPET_DB"])
        f.write("repet_port: %s\n" % os.environ["REPET_PORT"])
        f.write("repet_job_manager: SGE\n")
        f.close()
    
                    
#    def test_run_as_script_step1Step2Map(self):
#        #cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -m 'Map' -p %s -s %s -g %s -C %s" % (self._inPathTableName,self._RefTETableName, self._genomeTableName, self._configFileName)
#        cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -p %s -s %s -g %s -C %s" % (self.inPathTableName,self.RefTETableName, self.genomeTableName, self._configFileName)
#        subprocess.call(cmd, shell = True)
#        
#        cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 2 -p %s -s %s -g %s -C %s" % (self.inPathTableName,self.RefTETableName, self.genomeTableName, self._configFileName)
#        subprocess.call(cmd, shell = True)
#        
#        self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
        
        
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy))
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy))
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag))
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy))
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy))
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag))

#    def test_run_as_script_step2(self):
#        cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -p %s -s %s -g %s -C %s" % (self._inPathTableName,self._RefTETableName, self._genomeTableName, self._configFileName)
#        print cmd
#        subprocess.call(cmd, shell = True)
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy))
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy))
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag))
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy))
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy))
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag))
    
if __name__ == "__main__":
    unittest.main()