diff SMART/Java/Python/test/Test_F_mergeSlidingWindowsClusters.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_mergeSlidingWindowsClusters.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,80 @@
+import unittest
+import os
+from SMART.Java.Python.mergeSlidingWindowsClusters import MergeSlidingWindowsClusters
+from SMART.Java.Python.misc import Utils
+
+class Test_F_mergeSlidingWindowsClusters(unittest.TestCase):
+
+
+    def setUp(self):
+        self._outputFileName = 'outputMSWC'
+        self._inputFileName1 = 'inputMSWC1.gff3'
+        self._inputFileName2 = 'inputMSWC2.gff3'
+        self._writeInput1(self._inputFileName1)
+        self._writeInput2(self._inputFileName2)
+        self._expOutput = 'expOutputMSWC.gff3'
+        self._writeExpOutput(self._expOutput)
+
+    def tearDown(self):
+        os.remove(self._inputFileName1)
+        os.remove(self._inputFileName2)
+        os.remove(self._outputFileName+'.gff3')
+        os.remove(self._expOutput)
+
+
+    def test_run(self):
+        iMSWC = MergeSlidingWindowsClusters(0)
+        iMSWC.addInput(self._inputFileName1, 'gff3')
+        iMSWC.addInput(self._inputFileName2, 'gff3')
+        iMSWC.setOutput(self._outputFileName)
+        iMSWC.merge()
+        self.assertTrue(Utils.diff(self._outputFileName+'.gff3', self._expOutput))
+        
+    def test_run_asScript(self):
+        cmd = 'python ../mergeSlidingWindowsClusters.py -i %s -f gff3 -j %s -g gff3 -o outputMSWC.gff3 --galaxy -v 0' % (self._inputFileName1, self._inputFileName2)
+        os.system(cmd)
+        self.assertTrue(Utils.diff(self._outputFileName+'.gff3', self._expOutput)) 
+        
+    def _writeInput1(self, fileName):
+        f = open(fileName, 'w')
+        f.write("chr1\ttest\tmatch\t6155418\t6155441\t24\t+\t.\tName=test1/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100\n")
+        f.write("chr2\ttest\tmatch\t26303950\t26303981\t32\t+\t.\tName=test2/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93\n")
+        f.write("chr3\ttest\tmatch\t28320540\t28320574\t35\t+\t.\tName=test2/1;occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94\n")
+        f.write("chr4\ttest\tmatch\t28565007\t28565041\t35\t+\t.\tName=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88\n")
+        f.write("chr6\ttest\tmatch\t48565007\t48565041\t35\t+\t.\tName=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80\n")
+        f.close()
+
+    def _writeInput2(self, fileName):
+        f = open(fileName, 'w')
+        f.write("chr1\ttest\tmatch\t6155418\t6155441\t24\t+\t.\tName=test1/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100\n")
+        f.write("chr2\ttest\tmatch\t26303990\t26304021\t32\t+\t.\tName=test2/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93\n")
+        f.write("chr3\ttest\tmatch\t28320540\t28320574\t35\t+\t.\tName=test2/1;occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94\n")
+        f.write("chr4\ttest\tmatch\t28565017\t28565051\t35\t+\t.\tName=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88\n")
+        f.write("chr5\ttest\tmatch\t30000000\t30000050\t50\t+\t.\tName=test3/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=1;ID=test3/1-4;identity=50\n")
+        f.close()   
+        
+    def _writeExpOutput(self, fileName):
+        f = open(fileName, 'w')
+        f.write("""chr6	S-MART	match	48565007	48565041	35	+	.	occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80;Name=region_1
+chr5	S-MART	match	30000000	30000050	50	+	.	occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=1;ID=test3/1-4;identity=50;Name=region_2
+chr4	S-MART	match	28565017	28565051	35	+	.	occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=region_3
+chr4	S-MART	match	28565007	28565041	35	+	.	occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=region_4
+chr3	S-MART	match	28320540	28320574	35	+	.	occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=region_5
+chr2	S-MART	match	26303990	26304021	32	+	.	occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=region_6
+chr2	S-MART	match	26303950	26303981	32	+	.	occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=region_7
+chr1	S-MART	match	6155418	6155441	24	+	.	occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=region_8
+""")
+#       f.write("chr6\tS-MART\tmatch\t48565007\t48565041\t35\t+\t.\tName=region_1;occurrence=3;feature=match;rank=3;score=35;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80\n")
+#       f.write("chr5\tS-MART\tmatch\t30000000\t30000050\t50\t+\t.\tName=region_2;occurrence=3;feature=match;rank=3;score=50;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=1;ID=test3/1-4;identity=50\n")
+#       f.write("chr4\tS-MART\tmatch\t28565017\t28565051\t35\t+\t.\tName=region_3;occurrence=3;feature=match;rank=3;score=35;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88\n")
+#       f.write("chr4\tS-MART\tmatch\t28565007\t28565041\t35\t+\t.\tName=region_4;occurrence=3;feature=match;rank=3;score=35;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88\n")
+#       f.write("chr3\tS-MART\tmatch\t28320540\t28320574\t35\t+\t.\tName=region_5;occurrence=2;feature=match;score=35;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94\n")
+#       f.write("chr2\tS-MART\tmatch\t26303990\t26304021\t32\t+\t.\tName=region_6;occurrence=1;feature=match;rank=1;score=32;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93\n")
+#       f.write("chr2\tS-MART\tmatch\t26303950\t26303981\t32\t+\t.\tName=region_7;occurrence=1;feature=match;rank=1;score=32;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93\n")
+#       f.write("chr1\tS-MART\tmatch\t6155418\t6155441\t24\t+\t.\tName=region_8;occurrence=1;feature=match;rank=1;score=24;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100\n")
+        f.close()
+    
+            
+
+if __name__ == "__main__":
+    unittest.main()