diff smart_toolShed/commons/core/parsing/test/Test_BowtieParser.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/parsing/test/Test_BowtieParser.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,57 @@
+from commons.core.parsing.BowtieParser import BowtieParser
+import unittest, os
+
+
+class Test_BlatParser(unittest.TestCase):
+
+
+    def test_simple(self):
+        fileName = "tmpFile.bowtie"
+        handle   = open(fileName, "w")
+        handle.write("HWI-EAS179_0053:2:1:1365:7879#0/2\t+\tchrXHet\t191698\tACCGCTGAACCACTTTCATNCNTGGGATTGTGAACTGAAACTGTTCACATGAACTTGGAATTCCCAGTAAGTGTGA\tLcaYcacLaTdd`dacacYBaBTa^^TL^M`]`^aa`Tca`LaLTUa]a_bcLcTMMMMa^a^`bT`ccT_UbM_B\t0\t19:G>N,21:T>N\n")
+        handle.write("HWI-EAS179_0053:2:1:1365:7879#0/1\t-\tchrXHet\t191803\tCCCCTTGTACACACCGCCCGTCGCTACTACCGATTGAATTATGTAGTGAGGTCTCCGGACGTGATCACTGTGACGC\tBBBBBBBBB`O`DS]]aYabaaa[ULYLY]^b`^a^aZZZ_LLLca_a_b^^aYdbd``d^ccaY`_caccc^acc\t0\t33:T>G,72:T>C\n")
+        handle.write("HWI-EAS179_0053:2:1:1371:11420#0/2\t+\tchr3L\t16569206\tTATGAGCGCCAATTTTGCANTTTTATTTTTGTACAAGCCAAGGGTTTTGCAACATTCACAGCGCTTGCCACTTGTC\tcY^bcYLcaL]`]]`aaTaBaab^_ZZ__R[`[cYccc^Ybb^_L`L`Y`aM_a_TcTcc`LL]]MYaYabbTY`^\t0\t19:G>N\n")
+        handle.write("HWI-EAS179_0053:2:1:1371:11420#0/1\t-\tchr3L\t16569298\tAATGAACCATTGTAATTACCCACAACACATACAGTCACACACGAGATGCACACAAGTCGGAAACGGAAGCGAGACG\tBBBBBBBBBBBBBBBBBBBBBB^T`]Y^`KZY__LY_a]^T^ccYaYY__YT]VZbL]`b^cLT^a^caccYbT^b\t0\n")
+        handle.close()
+
+        parser = BowtieParser("tmpFile.bowtie", 0)
+        for cpt, mapping in enumerate(parser.getIterator()):
+            transcript = mapping.getTranscript()
+            if cpt == 0:
+                self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1365:7879#0/2")
+                self.assertEquals(transcript.getChromosome(), "chrXHet")
+                self.assertEquals(transcript.getDirection(), 1)
+                self.assertEquals(transcript.getStart(), 191699)
+                self.assertEquals(transcript.getEnd(), 191774)
+                self.assertEquals(transcript.getTagValue("nbMismatches"), 2)
+            elif cpt == 1:
+                self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1365:7879#0/1")
+                self.assertEquals(transcript.getChromosome(), "chrXHet")
+                self.assertEquals(transcript.getDirection(), -1)
+                self.assertEquals(transcript.getStart(), 191804)
+                self.assertEquals(transcript.getEnd(), 191879)
+                self.assertEquals(transcript.getTagValue("nbMismatches"), 2)
+            elif cpt == 2:
+                self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1371:11420#0/2")
+                self.assertEquals(transcript.getChromosome(), "chr3L")
+                self.assertEquals(transcript.getDirection(), 1)
+                self.assertEquals(transcript.getStart(), 16569207)
+                self.assertEquals(transcript.getEnd(), 16569282)
+                self.assertEquals(transcript.getTagValue("nbMismatches"), 1)
+            elif cpt == 3:
+                self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1371:11420#0/1")
+                self.assertEquals(transcript.getChromosome(), "chr3L")
+                self.assertEquals(transcript.getDirection(), -1)
+                self.assertEquals(transcript.getStart(), 16569299)
+                self.assertEquals(transcript.getEnd(), 16569374)
+                self.assertEquals(transcript.getTagValue("nbMismatches"), 0)
+            else:
+                self.fail()
+
+        os.remove(fileName)
+        
+        
+
+if __name__ == "__main__":
+    unittest.main()
+