Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/SMART/Java/Python/ncList/test/Test_F_FindOverlapsWithOneInterval.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/SMART/Java/Python/ncList/test/Test_F_FindOverlapsWithOneInterval.py Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,121 @@ +import unittest +import struct +import os +from SMART.Java.Python.structure.Interval import Interval +from SMART.Java.Python.ncList.FindOverlapsWithOneInterval import FindOverlapsWithOneInterval +from SMART.Java.Python.misc import Utils + +class Test_F_FindOverlapsWithOneInterval(unittest.TestCase): + + def setUp(self): + self._inputGff3FileName = 'sortedFile.gff3' + self._writeGFF3File(self._inputGff3FileName) + self._obsFileName = "overlap.gff3" + self._expFileName = "expFile.gff3" + self._iFOWOI = FindOverlapsWithOneInterval(0) + self._iFOWOI.setFileName(self._inputGff3FileName, "gff3") + self._iFOWOI.setOutputFileName(self._obsFileName) + + def tearDown(self): + os.remove(self._inputGff3FileName) + os.remove(self._obsFileName) + os.remove(self._expFileName) + + def test_run_general(self): + self._iFOWOI.setInterval("chr1", 500, 850) + self._iFOWOI.run() + self._writeExpGFF3File_general(self._expFileName) + self.assertTrue(Utils.diff(self._expFileName, self._obsFileName)) + +# def test_run_general_asScript(self): +# cmd = 'python ../FindOverlapsWithOneInterval.py -i %s -f gff3 -o %s -c chr1 -s 500 -e 850 -v 0' % (self._inputGff3FileName, self._obsFileName) +# os.system(cmd) +# self._writeExpGFF3File_general(self._expFileName) +# self.assertTrue(Utils.diff(self._expFileName, self._obsFileName)) +# +# def test_run_one_overlap(self): +# self._iFOWOI.setInterval("chr1", 1250, 1450) +# self._iFOWOI.run() +# self._writeExpGFF3File_one_overlap(self._expFileName) +# self.assertTrue(Utils.diff(self._expFileName, self._obsFileName)) +# +# def test_run_one_overlap_asScript(self): +# cmd = 'python ../FindOverlapsWithOneInterval.py -i %s -f gff3 -o %s -c chr1 -s 1250 -e 1450 -v 0' % (self._inputGff3FileName, self._obsFileName) +# os.system(cmd) +# self._writeExpGFF3File_one_overlap(self._expFileName) +# self.assertTrue(Utils.diff(self._expFileName, self._obsFileName)) +# +# def test_run_all_overlap(self): +# self._iFOWOI.setInterval("chr1", 300, 1250) +# self._iFOWOI.run() +# self._writeExpGff3File_all_overlap(self._expFileName) +# self.assertTrue(Utils.diff(self._expFileName, self._obsFileName)) +# +# def test_run_all_overlap_asScript(self): +# cmd = 'python ../FindOverlapsWithOneInterval.py -i %s -f gff3 -o %s -c chr1 -s 300 -e 1250 -v 0' % (self._inputGff3FileName, self._obsFileName) +# os.system(cmd) +# self._writeExpGff3File_all_overlap(self._expFileName) +# self.assertTrue(Utils.diff(self._expFileName, self._obsFileName)) +# +# def test_run_no_overlap_right(self): +# self._iFOWOI.setInterval("chr1", 1400, 1500) +# self._iFOWOI.run() +# f = open(self._expFileName, "w") +# f.close() +# self.assertTrue(Utils.diff(self._expFileName, self._obsFileName)) +# +# def test_run_no_overlap_right_asScript(self): +# cmd = 'python ../FindOverlapsWithOneInterval.py -i %s -f gff3 -o %s -c chr1 -s 1400 -e 1500 -v 0' % (self._inputGff3FileName, self._obsFileName) +# os.system(cmd) +# f = open(self._expFileName, "w") +# f.close() +# self.assertTrue(Utils.diff(self._expFileName, self._obsFileName)) +# +# def test_run_no_overlap_left(self): +# self._iFOWOI.setInterval("chr1", 0, 8) +# self._iFOWOI.run() +# f = open(self._expFileName, "w") +# f.close() +# self.assertTrue(Utils.diff(self._expFileName, self._obsFileName)) +# +# def test_run_no_overlap_left_asScript(self): +# cmd = 'python ../FindOverlapsWithOneInterval.py -i %s -f gff3 -o %s -c chr1 -s 0 -e 8 -v 0' % (self._inputGff3FileName, self._obsFileName) +# os.system(cmd) +# f = open(self._expFileName, "w") +# f.close() +# self.assertTrue(Utils.diff(self._expFileName, self._obsFileName)) + + def _writeExpGff3File_all_overlap(self, fileName): + f = open(fileName, 'w') + f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n") + f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n") + f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n") + f.write("chr1\tS-MART\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n") + f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n") + f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n") + f.write("chr1\tS-MART\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n") + f.close() + + def _writeExpGFF3File_one_overlap(self, fileName): + f = open(fileName, "w") + f.write("chr1\tS-MART\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n") + f.close() + + def _writeExpGFF3File_general(self, fileName): + f = open(fileName, "w") + f.write("chr1\tS-MART\ttranscript\t500\t850\t.\t+\t.\tnbOverlaps=4;overlapsWith=test2.1--test2.3--test2.5--test2.6\n") + f.close() + + def _writeGFF3File(self, fileName): + f = open(fileName, "w") + f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n") + f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n") + f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n") + f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n") + f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n") + f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n") + f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n") + f.close() + +if __name__ == "__main__": + unittest.main()