--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/test/Test_FastaParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,75 @@
+from commons.core.parsing.FastaParser import FastaParser
+from SMART.Java.Python.structure.Sequence import Sequence
+import unittest
+
+class Test_FastaParser(unittest.TestCase):
+
+    def test_getSubsequence(self):
+        fastaFile = "myFastaInput.fasta"
+        self._writeInputFastaFile(fastaFile)
+        parser = FastaParser(fastaFile)
+        chromosome = "1"
+        expSeq = Sequence("1:1-20 (1)", "CCTAAGCCATTGCTTGGTGA")
+        obsSeq = parser.getSubSequence(chromosome, 1, 20, 1)
+        self.assertEquals(expSeq, obsSeq)
+
+    def test_getSubsequence_long_sequence(self):
+        fastaFile = "myFastaInput.fasta"
+        self._writeInputFastaFile(fastaFile)
+        parser = FastaParser(fastaFile)
+        chromosome = "2"
+        expSeq = Sequence("subsequence", "TGAAGA")
+        obsSeq = parser.getSubSequence(chromosome, 55, 60, 1, "subsequence")
+        self.assertEquals(expSeq, obsSeq)
+
+    def test_getSubsequence_long_sequence_inside_and_outside(self):
+        fastaFile = "myFastaInput.fasta"
+        self._writeInputFastaFile(fastaFile)
+        parser = FastaParser(fastaFile)
+        chromosome = "2"
+        expSeq = Sequence("subsequence", "TTA")
+        obsSeq = parser.getSubSequence(chromosome, 137, 151, 1, "subsequence")
+        self.assertEquals(expSeq, obsSeq)
+
+    def test_getSubsequence_long_sequence_last_letter(self):
+        fastaFile = "myFastaInput.fasta"
+        self._writeInputFastaFile(fastaFile)
+        parser = FastaParser(fastaFile)
+        chromosome = "2"
+        expSeq = Sequence("subsequence", "A")
+        obsSeq = parser.getSubSequence(chromosome, 139, 151, 1, "subsequence")
+        self.assertEquals(expSeq, obsSeq)
+
+    def test_getSubsequence_long_sequence_totally_outside(self):
+        fastaFile = "myFastaInput.fasta"
+        self._writeInputFastaFile(fastaFile)
+        parser = FastaParser(fastaFile)
+        chromosome = "2"
+        isSysExit = False
+        try:
+            parser.getSubSequence(chromosome, 140, 151, 1, "subsequence")
+        except:
+            isSysExit = True
+        self.assertTrue(isSysExit)
+        
+    def test_setTags(self):
+        fastaFile = "myFastaInput.fasta"
+        self._writeInputFastaFile(fastaFile)
+        parser = FastaParser(fastaFile)
+        parser.setTags()
+        expTags = {"1" : 0,
+                   "2" : 54}
+        obsTags = parser.getTags()
+        self.assertEquals(expTags, obsTags)
+        
+    def _writeInputFastaFile(self, fastaFile):
+        myHandler = open(fastaFile, 'w')
+        myHandler.write(">1\n")
+        myHandler.write("CCTAAGCCATTGCTTGGTGATTATGAAGGCAGTAGTCAAACCTCCACAAT\n")
+        myHandler.write(">2\n")
+        myHandler.write("TATGAGATCAACAGGGGCTTTGCTAGCCTGAGGGCGATTGGTCAAGGCCG\n")
+        myHandler.write("GACCTGAAGAAATTCCTGATTGTACGTTCTGGTTACTCTTCAATTTGGGC\n")
+        myHandler.write("TGCTTAATTATCTCCTCAATTTCAATTTGGCCATGCTTA\n")
+
+if __name__ == "__main__":
+    unittest.main()