diff smart_toolShed/commons/core/parsing/test/Test_BedParser.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_BedParser.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,58 @@
+import unittest, os
+from commons.core.parsing.BedParser import BedParser
+
+
+class Test_BedParser(unittest.TestCase):
+    
+    def test_Parser(self):
+        parser = BedParser("data/testBedParser1.bed")
+
+        self.assertEqual(parser.getNbTranscripts(), 1)
+
+        for transcript in parser.getIterator():
+            self.assertEqual(transcript.getChromosome(), "arm_X")
+            self.assertEqual(transcript.getName(), "test1.1")
+            self.assertEqual(transcript.getStart(), 1000)
+            self.assertEqual(transcript.getEnd(), 2999)
+            self.assertEqual(transcript.getDirection(), 1)
+            self.assertEqual(transcript.getNbExons(), 2)
+            exons = transcript.getExons()
+            self.assertEqual(exons[0].getChromosome(), "arm_X")
+            self.assertEqual(exons[0].getStart(), 1000)
+            self.assertEqual(exons[0].getEnd(), 1099)
+            self.assertEqual(exons[0].getDirection(), 1)
+            self.assertEqual(exons[1].getChromosome(), "arm_X")
+            self.assertEqual(exons[1].getStart(), 2000)
+            self.assertEqual(exons[1].getEnd(), 2999)
+            self.assertEqual(exons[1].getDirection(), 1)
+
+    def test_Parser_short(self):
+        tmpFileName = "tmpFile.bed"
+        tmpHandle   = open(tmpFileName, "w")
+        tmpHandle.write("""X\t554748\t554904\texon
+X\t554748\t554904\tCDS
+X\t554748\t554750\tstart_codon
+""")
+        tmpHandle.close()
+        parser = BedParser(tmpFileName)
+        self.assertEqual(parser.getNbTranscripts(), 3)
+        for cpt, transcript in enumerate(parser.getIterator()):
+            self.assertEqual(transcript.getNbExons(), 1)
+            self.assertEqual(transcript.getChromosome(), "X")
+            self.assertEqual(transcript.getStart(), 554748)
+            if cpt == 0:
+                self.assertEqual(transcript.getEnd(), 554903)
+                self.assertEqual(transcript.getName(), "exon")
+            elif cpt == 1:
+                self.assertEqual(transcript.getEnd(), 554903)
+                self.assertEqual(transcript.getName(), "CDS")
+            elif cpt == 2:
+                self.assertEqual(transcript.getEnd(), 554749)
+                self.assertEqual(transcript.getName(), "start_codon")
+        os.remove(tmpFileName)
+
+
+
+if __name__ == '__main__':
+        unittest.main()
+