diff SMART/Java/Python/test/Test_F_mapperAnalyzer.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_mapperAnalyzer.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,55 @@
+import unittest
+import os, glob
+from SMART.Java.Python.mapperAnalyzer import MapperAnalyzer
+from commons.core.parsing.GffParser import GffParser
+
+class Test_F_mapperAnalyzer(unittest.TestCase):
+
+    def setUp(self):
+        self.readsFileName   = "inputFile.fastq"
+        self.mappingFileName = "inputFile.sam"
+        self.outputFileName  = "outputFile.gff3"
+         
+    def tearDown(self):
+        for fileRoot in (self.readsFileName, self.mappingFileName, self.outputFileName):
+            for file in glob.glob("%s*" % (fileRoot)):
+                os.remove(file)
+        os.system("rm tmpNames_* tmpSequences_* smartdb*")
+
+    def test_run_simple(self):
+        handle = open(self.readsFileName, "w")
+        handle.write("@read1\n")
+        handle.write("AAAAAAAAAAAAAAAAAAAA\n")
+        handle.write("+\n")
+        handle.write("AAAAAAAAAAAAAAAAAAAA\n")
+        handle.write("@read2\n")
+        handle.write("CCCCCCCCCCCCCCCCCCCC\n")
+        handle.write("+\n")
+        handle.write("AAAAAAAAAAAAAAAAAAAA\n")
+        handle.close()
+        handle = open(self.mappingFileName, "w")
+        handle.write("read1\t0\tchr1\t1\t30\t20M\t*\t0\t0\tAAAAAAAAAAAAAAAAAAAA\tAAAAAAAAAAAAAAAAAAAA\tNM:i:0\n")
+        handle.write("read2\t0\tchr2\t1\t30\t20M\t*\t0\t0\tCCCCCCCCCCCCCCCCCCCC\tAAAAAAAAAAAAAAAAAAAA\tNM:i:0\n")
+        handle.write("read2\t0\tchr3\t1\t30\t20M\t*\t0\t0\tCCCCCCCCCCCCCCCCCCCC\tAAAAAAAAAAAAAAAAAAAA\tNM:i:0\n")
+        handle.close()
+        analyzer = MapperAnalyzer(0)
+        analyzer.setMappingFile(self.mappingFileName, "sam")
+        analyzer.setSequenceFile(self.readsFileName, "fastq")
+        analyzer.setOutputFile(self.outputFileName, "S-MART")
+        analyzer.setMaxMappings(1)
+        analyzer.mergeExons(True)
+        analyzer.analyze()
+
+        parser = GffParser(self.outputFileName)
+        self.assertEqual(parser.getNbTranscripts(), 1)
+        for transcript in parser.getIterator():
+            self.assertEqual(transcript.getName(), "read1")
+            self.assertEqual(transcript.getChromosome(), "chr1")
+            self.assertEqual(transcript.getStart(), 1)
+            self.assertEqual(transcript.getEnd(), 20)
+            self.assertEqual(transcript.getDirection(), 1)
+            
+        
+if __name__ == "__main__":
+    unittest.main()
+