diff commons/tools/tests/Test_F_LaunchBlasterInParallel.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/tests/Test_F_LaunchBlasterInParallel.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,116 @@
+from commons.core.utils.FileUtils import FileUtils
+import unittest
+import os
+import shutil
+from commons.tools.LaunchBlasterInParallel import LaunchBlasterInParallel
+
+class Test_F_LaunchBlasterInParallel(unittest.TestCase):
+
+    CLUSTER_HOST = "compute-2-46.local"
+
+    def setUp(self):
+        self._inFilePath = "%s/Tools/DmelChr4_chunks.fa" % os.environ["REPET_DATA"]
+        self._configFileName = "TE.cfg"
+        self._outputFileName = "out.align.not_over"
+
+    def tearDown(self):
+        try:
+            os.remove(self._outputFileName)
+            os.remove(self._configFileName)
+        except:
+            pass
+
+    def test_run_as_script_1bank_1file_withoutABA(self):
+        self._outputFileName = "out.align"
+        os.mkdir("tmp")
+        os.chdir("tmp")
+        queryFileName = "chunks.fa"
+        with open(queryFileName, "w") as f:
+            f.write(">chunk1\n")
+            f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
+            f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
+        os.chdir("..")
+        subjectFileName = "genome.fa"
+        with open(subjectFileName, "w") as f:
+            f.write(">chunk1\n")
+            f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
+            f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
+            f.write(">chunk2\n")
+            f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
+            f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
+        expFileName = "expected"
+        with open(expFileName, "w") as f:
+            f.write("chunk1\t1\t120\tchunk1\t1\t120\t4e-68\t238\t100\n")
+            f.write("chunk1\t1\t120\tchunk2\t1\t120\t4e-68\t238\t100\n")
+        self._writeConfig(0.1)
+        
+        cmd = "LaunchBlasterInParallel.py -q %s/tmp -s %s/%s -C %s -o %s" % (os.getcwd(), os.getcwd(), subjectFileName, self._configFileName, self._outputFileName)
+        os.system(cmd)
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
+        FileUtils.removeFilesByPattern("*.param")
+        shutil.rmtree("tmp")
+        os.remove(subjectFileName)
+        os.remove(expFileName)
+        
+    def test_run_as_script_1bank_2_batches(self):
+        os.mkdir("tmp")
+        os.chdir("tmp")
+        os.symlink("%s/Tools/batches/batch_1.fa" % os.environ["REPET_DATA"], "batch_1.fa")
+        os.symlink("%s/Tools/batches/batch_2.fa" % os.environ["REPET_DATA"], "batch_2.fa")
+        os.chdir("..")
+        
+        expFileName = "%s/Tools/DmelChr4.align.not_over" % os.environ["REPET_DATA"]
+        self._writeConfig()
+        
+        cmd = "LaunchBlasterInParallel.py -q %s/tmp -s %s -a -o %s -C %s" % (os.getcwd(), self._inFilePath, self._outputFileName, self._configFileName)
+        os.system(cmd)
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
+        FileUtils.removeFilesByPattern("*.param")
+        shutil.rmtree("tmp")
+        
+    def test_run_1bank_1bank_2_batches(self):
+        os.mkdir("tmp")
+        os.chdir("tmp")
+        os.symlink("%s/Tools/batches/batch_1.fa" % os.environ["REPET_DATA"], "batch_1.fa")
+        os.symlink("%s/Tools/batches/batch_2.fa" % os.environ["REPET_DATA"], "batch_2.fa")
+        os.chdir("..")
+        
+        expFileName = "%s/Tools/DmelChr4.align.not_over" % os.environ["REPET_DATA"]
+        self._writeConfig()
+        
+        iLaunchBlaster = LaunchBlasterInParallel(configFileName = self._configFileName, outFileName = self._outputFileName)
+        iLaunchBlaster.setDoAllByall(True)
+        iLaunchBlaster.setVerbosity(4)
+        iLaunchBlaster.setQueryDirectory("%s/tmp" % os.getcwd())
+        iLaunchBlaster.setSubjectFilePath(self._inFilePath)
+        iLaunchBlaster.run()
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
+        FileUtils.removeFilesByPattern("*.param")
+        shutil.rmtree("tmp")
+        
+    def _writeConfig(self, eValue = 1e-300):
+        with open(self._configFileName, "w") as fh:
+            fh.write("[jobs]\n")
+            if os.getenv("HOSTNAME") == self.CLUSTER_HOST:
+                fh.write("resources: test\n")
+            else:
+                fh.write("resources:\n")
+            fh.write("tmpDir:\n")
+            fh.write("copy: no\n") 
+            fh.write("clean: yes\n")
+            fh.write("\n")
+            fh.write("[prepare_data]\n")
+            fh.write("chunk_length: 200000\n")
+            fh.write("chunk_overlap: 10000\n")
+            fh.write("\n")
+            fh.write("[alignment]\n")
+            fh.write("blast: ncbi\n")
+            fh.write("Evalue: %s\n" % eValue)
+            fh.write("length: 100\n")
+            fh.write("identity: 90\n")
+
+if __name__ == "__main__":
+    unittest.main()
\ No newline at end of file