view commons/tools/tests/Test_F_TEclassifierPE.py @ 31:0ab839023fe4

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import os
import unittest
from commons.tools.TEclassifierPE import TEclassifierPE
from commons.core.utils.FileUtils import FileUtils
from commons.core.sql.DbFactory import DbFactory

class Test_F_TEclassifierPE(unittest.TestCase):

    def test_run(self):
        projectName = "dummy"
        configFileName = "dummy.cfg"
        self.writeConfigFile(configFileName, projectName)
        inputFileName = "dummy.fa"
        with open(inputFileName, "w") as f:
            f.write(">dummySSR\n")
            f.write("AGTTACCATGCCCAGCATTAACCCCCCTCAACAACCACCTCCGCCTATGAAGCCCGCCCG\n")
            f.write("AGTTACCATGCCCAGCATTAACCCCCCTCAACAACCACCTCCGCCTATGAAGCCCGCCCG\n")
        expFileName = "exp.classif"
        with open(expFileName, "w") as f:
            f.write("dummySSR\t120\t.\tok\tNA\tSSR\tNA\tCI=100; struct=(TElength: <150bps; SSRCoverage=0.00)\n")
        obsFileName = "%s.classif" % projectName
        statsFileName = "%s.classif_stats.txt" % projectName
        analysisFileName = "%s.SSR.set" % inputFileName
            
        iTEclassifierPE = TEclassifierPE(inputFileName, configFileName, doClean = True)
        iTEclassifierPE.run()
        
        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
        
        iDb = DbFactory.createInstance()
        iDb.dropTable("%s_TR_set" % projectName)
        iDb.dropTable("%s_polyA_set" % projectName)
        iDb.dropTable("%s_ORF_map" % projectName)
        iDb.dropTable("%s_SSR_set" % projectName)
        iDb.close()
        os.remove(configFileName)
        os.remove(inputFileName)
        os.remove(expFileName)
        os.remove(obsFileName)
        os.remove(statsFileName)
        os.remove(analysisFileName)
        
    def writeConfigFile(self, fileName, projectName):
        with open(fileName, "w") as f:
            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("\n")
            f.write("[project]\n")
            f.write("project_name: %s\n" % projectName)
            f.write("project_dir: %s\n" % os.getcwd())
            f.write("\n")
            f.write("[detect_features]\n")
            f.write("clean: yes\n")
            f.write("blast: ncbi\n")
            f.write("term_rep: no\n")
            f.write("polyA: no\n")
            f.write("tand_rep: yes\n")
            f.write("orf: no\n")
            f.write("TE_HMMER: no\n")
            f.write("TE_BLRtx: no\n")
            f.write("TE_BLRn: no\n")
            f.write("TE_BLRx: no\n")
            f.write("HG_BLRn: no\n")
            f.write("rDNA_BLRn: no\n") 
            f.write("tRNA_scan: no\n")
            f.write("TRFmaxPeriod: 15\n")
            f.write("\n")
            f.write("[classif_consensus]\n")
            f.write("max_profiles_evalue: 1e-3\n")
            f.write("min_TE_profiles_coverage: 20\n")
            f.write("min_HG_profiles_coverage: 75\n")
            f.write("max_helitron_extremities_evalue: 1e-3\n")
            f.write("min_TE_bank_coverage: 5\n")
            f.write("min_HG_bank_coverage: 95\n")
            f.write("min_rDNA_bank_coverage: 95\n")
            f.write("min_HG_bank_identity: 90\n")
            f.write("min_rDNA_bank_identity: 90\n")
            f.write("min_SSR_coverage: 0.75\n")
            f.write("max_SSR_size: 150\n")
            f.write("clean: yes\n")
            
if __name__ == "__main__":
    unittest.main()