diff commons/launcher/tests/Test_F_LaunchTallymer.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/tests/Test_F_LaunchTallymer.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,151 @@
+import unittest
+import os
+from commons.core.utils.FileUtils import FileUtils
+import shutil
+from commons.launcher.LaunchTallymer import LaunchTallymer
+
+class Test_F_LaunchTallymer(unittest.TestCase):
+
+    def setUp(self):
+        self._inFastaFileName = "%s/Tools/DmelChr4.fa" % os.environ["REPET_DATA"]
+
+    def test_run_output_as_gff_cleaned(self):
+        iLaunchTallymer = LaunchTallymer(self._inFastaFileName,  clean = True, verbosity=2)
+        iLaunchTallymer.run()
+        
+        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
+        obsFileName = "DmelChr4.tallymer.gff"
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        os.remove(obsFileName)
+        os.remove("DmelChr4.tallymer.stat")
+        
+    def test_run_with_remote_dir(self):
+        os.makedirs("sourceDir")
+        changedInFastaFileName = os.path.basename(self._inFastaFileName)
+        changedInFastaFilepath = os.path.join("sourceDir",changedInFastaFileName)
+        shutil.copy2(self._inFastaFileName, changedInFastaFilepath)
+        
+        iLaunchTallymer = LaunchTallymer(changedInFastaFilepath,  clean = True, verbosity=2)
+        iLaunchTallymer.run()
+        
+        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
+        obsFileName = "DmelChr4.tallymer.gff"
+        
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        obsSourceDirFiles = os.listdir("sourceDir")
+        expSourceDirFiles = [changedInFastaFileName,]
+        self.assertEquals(expSourceDirFiles, obsSourceDirFiles)
+        
+        os.remove(obsFileName)
+        os.remove("DmelChr4.tallymer.stat")
+        shutil.rmtree("sourceDir")
+
+
+    def test_run_output_as_gff_cleaned_changed_minOccs2(self):
+        iLaunchTallymer = LaunchTallymer(self._inFastaFileName, minOccs=2, clean = True, verbosity=2)
+        iLaunchTallymer.run()
+        
+        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20_minOcc2.gff" % os.environ["REPET_DATA"]
+        obsFileName = "DmelChr4.tallymer.gff"
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        os.remove(obsFileName)
+        os.remove("DmelChr4.tallymer.stat")
+        
+    def test_run_output_as_gff_cleaned_relative_input(self):
+        srcFastaFileName = self._inFastaFileName
+        dstFastaFileName = os.path.basename(self._inFastaFileName)
+        shutil.copy2(srcFastaFileName, dstFastaFileName)
+        iLaunchTallymer = LaunchTallymer(dstFastaFileName,  clean = True, verbosity=2)
+        iLaunchTallymer.run()
+        
+        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
+        obsFileName = "DmelChr4.tallymer.gff"
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        
+        os.remove(obsFileName)
+        os.remove("DmelChr4.tallymer.stat")
+        os.remove(dstFastaFileName)
+   
+    def test_run_as_script_output_as_gff_cleaned_relative_input_(self):
+        srcFastaFileName = self._inFastaFileName
+        dstFastaFileName = os.path.basename(self._inFastaFileName)
+        shutil.copy2(srcFastaFileName, dstFastaFileName)
+        
+        cmd = 'LaunchTallymer.py -i %s -s 20 -c -v 3' % (self._inFastaFileName)
+        os.system(cmd)
+        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
+        obsFileName = "DmelChr4.tallymer.gff"
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        
+        os.remove(obsFileName)
+        os.remove("DmelChr4.tallymer.stat")
+        os.remove(dstFastaFileName)
+        
+    def test_run_output_as_wig_cleaned(self):
+        iLaunchTallymer = LaunchTallymer(self._inFastaFileName, outputFormats="wig", clean=True)
+        iLaunchTallymer.run()
+        
+        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.wig" % os.environ["REPET_DATA"]
+        obsFileName = "DmelChr4.tallymer.wig"
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        
+        os.remove(obsFileName)
+        os.remove("DmelChr4.tallymer.stat")
+
+    def test_run_output_as_gff_and_wig_k15_cleaned(self):
+        iLaunchTallymer = LaunchTallymer(self._inFastaFileName, merSize=15, outputFormats="wig,gff3", clean=True)
+        iLaunchTallymer.run()
+        
+        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.wig" % os.environ["REPET_DATA"]
+        obsFileName = "DmelChr4.tallymer.wig"
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        os.remove(obsFileName)
+        
+        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.gff3" % os.environ["REPET_DATA"]
+        obsFileName = "DmelChr4.tallymer.gff3"
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        os.remove(obsFileName)
+        
+        os.remove("DmelChr4.tallymer.stat")
+
+    def test_run_as_script_run_output_as_gff_and_wig_k15_cleaned(self):
+        logFileName = "test.log"
+        cmd = 'LaunchTallymer.py -i %s -s 15 -f gff,wig,vero -c -v 3 > %s' % (self._inFastaFileName, logFileName)
+        os.system(cmd)
+               
+        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.wig" % os.environ["REPET_DATA"]
+        obsFileName = "DmelChr4.tallymer.wig"
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        os.remove(obsFileName)
+        
+        expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.gff3" % os.environ["REPET_DATA"]
+        obsFileName = "DmelChr4.tallymer.gff"
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        os.remove(obsFileName)
+        
+        expLogFileName = "exp.log"
+        with open(expLogFileName, "w") as f:
+            f.write(" LaunchTallymer - WARNING - Warning: ignoring invalid formats: <vero>\n")
+            f.write(" LaunchTallymer - INFO - Starting to run tallymer search of sequence DmelChr4.fa \n")
+            f.write(" LaunchTallymer - INFO - Finished running tallymer scan of sequence DmelChr4.fa \n")
+            f.write(" LaunchTallymer - INFO - Starting to run tallymer search to map conversion\n")
+            f.write(" LaunchTallymer - INFO - Finished tallymer search to map conversion\n")
+            f.write(" LaunchTallymer - INFO - Generating wig file\n")
+            f.write(" LaunchTallymer - INFO - Generating gff file\n")
+        obsLogFileName = "obs.log"
+        os.system("cut -d'-' -f4,5,6 %s > %s" % (logFileName, obsLogFileName))
+        self.assertTrue(FileUtils.are2FilesIdentical(expLogFileName, obsLogFileName))
+        
+        os.remove(logFileName)
+        os.remove(expLogFileName)
+        os.remove(obsLogFileName)
+        os.remove("DmelChr4.tallymer.stat")
+        
+if __name__ == "__main__":
+    unittest.main()
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