diff commons/pyRepetUnit/hmmer/tests/TestHmmpfamAndParse2alignLauncher.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/tests/TestHmmpfamAndParse2alignLauncher.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,87 @@
+import unittest
+import os
+import sys
+
+if not os.environ.has_key( "REPET_PATH" ):
+    print "*** Error: no environment variable REPET_PATH"
+    sys.exit(1)
+sys.path.append( os.environ["REPET_PATH"] )
+
+from pyRepet.launcher.Launcher import HmmpfamAndParse2alignLauncher
+from pyRepet.sql.RepetJobMySQL import *
+
+class TestHmmpfamAndParse2alignLauncher(unittest.TestCase):
+    
+    def testConstructor(self):
+        
+        params = {
+                  "query" : "toto",
+                  "job_table":"fakeTable", 
+                  "queue" : "fakeQueue", 
+                  "groupid" : "fakeId",
+                  "tmpDir" : "fakeDir",
+                  "cDir" : "."
+        }
+      
+        hmmpfam = HmmpfamAndParse2alignLauncher("toto", params)
+        
+        self.assertEquals("toto", hmmpfam.query)
+        self.assertEquals("fakeTable", hmmpfam.job_table)
+        self.assertEquals("fakeQueue", hmmpfam.queue)
+        self.assertEquals("fakeId", hmmpfam.groupid)
+        self.assertEquals("fakeDir", hmmpfam.tmpdir)
+       
+       
+    def testCmd_start(self):
+        
+        fullInFileName = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa"
+        expectedCmdStart = "hmmpfam --informat FASTA -E 10 /workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms test_input_aa.fa > /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut"
+
+        user = "oinizan"
+        host = "pisano"
+        passwd = "oinizan"
+        dbName = "repet_oinizan"
+        jobDb = RepetJob(user , host , passwd , dbName)
+        params = {"param":"--informat FASTA -E 10",
+                  "query" : "toto",
+                  "job_table":"fake", 
+                  "queue" : "fake", 
+                  "groupid" : "fake",
+                  "profilDB": "/workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms",
+                  "tmpDir" : "fakeDir", 
+                  "outputDir": "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas",
+                  "scriptToLaunch": "/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py", 
+                  "cDir" : "."
+        }
+        self.hmmpfam = HmmpfamAndParse2alignLauncher(jobDb, params)
+        self.assertEquals(expectedCmdStart, self.hmmpfam.cmd_start ( fullInFileName ))    
+        
+        
+    def testCmd_finish(self):  
+        
+        fullInFileName = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa"
+        user = "oinizan"
+        host = "pisano"
+        passwd = "oinizan"
+        dbName = "repet_oinizan"
+        jobDb = RepetJob(user , host , passwd , dbName)
+        params = {"param":"--informat FASTA -E 10",
+                  "query" : "toto",
+                  "job_table":"fake", 
+                  "queue" : "fake", 
+                  "groupid" : "fake",
+                  "profilDB": "/workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms",
+                  "tmpDir" : "fakeDir", 
+                  "outputDir": "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas",
+                  "scriptToLaunch": "/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py",
+                  "cDir" : "."
+        }
+        self.hmmpfamAndParse2align = HmmpfamAndParse2alignLauncher(jobDb, params)
+        expectedCmdFinish = "os.system( \"/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py -i /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut -o /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut.align -c\" )\n"
+        self.assertEquals(expectedCmdFinish, self.hmmpfamAndParse2align.cmd_finish ( fullInFileName ))
+
+
+
+if __name__ == "__main__":                 
+	unittest.main()
+