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view SMART/Java/Python/ncList/test/Test_F_FindOverlapsWithSeveralIntervals.py @ 6:769e306b7933
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author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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import unittest import os, os.path from SMART.Java.Python.ncList.FindOverlapsWithSeveralIntervals import FindOverlapsWithSeveralIntervals from SMART.Java.Python.misc import Utils class Test_F_FindOverlapsWithSeveralIntervals(unittest.TestCase): def setUp(self): self._inputRefGff3FileName = 'sorted_Ref.gff3' self._inputQueryGff3FileName = 'sorted_Query.gff3' self._outputGff3FileName = 'output.gff3' self._expOutputFileName = 'expOutGff3.gff3' self._writeQueryGff3File(self._inputQueryGff3FileName) self._writeGFF3File(self._inputRefGff3FileName) self._iFOWSI = FindOverlapsWithSeveralIntervals(0) self._iFOWSI.setRefFileName(self._inputRefGff3FileName, "gff3") self._iFOWSI.setQueryFileName(self._inputQueryGff3FileName, "gff3") self._iFOWSI.setOutputFileName(self._outputGff3FileName) self._iFOWSI.prepareIntermediateFiles() self._iFOWSI.createNCLists() def tearDown(self): for fileName in (self._inputRefGff3FileName, self._inputQueryGff3FileName, self._outputGff3FileName, self._expOutputFileName): if os.path.exists(fileName): os.remove(fileName) def test_run_general(self): self._writeQueryGff3File(self._inputQueryGff3FileName) self._writeGFF3File(self._inputRefGff3FileName) self._iFOWSI = FindOverlapsWithSeveralIntervals(0) self._iFOWSI.setRefFileName(self._inputRefGff3FileName, "gff3") self._iFOWSI.setQueryFileName(self._inputQueryGff3FileName, "gff3") self._iFOWSI.setOutputFileName(self._outputGff3FileName) self._iFOWSI.prepareIntermediateFiles() self._iFOWSI.createNCLists() self._iFOWSI.compare() self._iFOWSI.close() self._writeExpOutFile_general(self._expOutputFileName) self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName)) def test_run_general_asScript(self): cmd = 'python ../FindOverlapsWithSeveralIntervals.py -i %s -f gff3 -j %s -g gff3 -o %s -v 0' % (self._inputQueryGff3FileName, self._inputRefGff3FileName, self._outputGff3FileName) os.system(cmd) self._writeExpOutFile_general(self._expOutputFileName) self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName)) def test_run_overlap_special_case(self): inputQueryGff3FileName = 'query2.gff3' self._writeQueryGff3File2(inputQueryGff3FileName) self._iFOWSI = FindOverlapsWithSeveralIntervals(0) self._iFOWSI.setRefFileName(self._inputRefGff3FileName, "gff3") self._iFOWSI.setQueryFileName(inputQueryGff3FileName, "gff3") self._iFOWSI.setOutputFileName(self._outputGff3FileName) self._iFOWSI.prepareIntermediateFiles() self._iFOWSI.createNCLists() self._iFOWSI.compare() self._iFOWSI.close() self._writeExpOutFile_special_case(self._expOutputFileName) self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName)) os.remove(inputQueryGff3FileName) def test_run_overlap_special_case_asScript(self): inputQueryGff3FileName = 'query2.gff3' self._writeQueryGff3File2(inputQueryGff3FileName) cmd = 'python ../FindOverlapsWithSeveralIntervals.py -i %s -f gff3 -j %s -g gff3 -o %s -v 0' % (inputQueryGff3FileName, self._inputRefGff3FileName, self._outputGff3FileName) os.system(cmd) self._writeExpOutFile_special_case(self._expOutputFileName) self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName)) os.remove(inputQueryGff3FileName) def _writeExpOutFile_special_case(self, fileName): f = open(fileName, 'w') f.write("chr1 S-MART test2 1250 1300 781 + . nbOverlaps=1;overlapsWith=test2.7;ID=query_2;Name=test1.2\n") f.close() def _writeExpOutFile_general(self, fileName): f = open(fileName, 'w') f.write("""chr1 S-MART test1.1 25 150 126 + . nbOverlaps=3;overlapsWith=test2.1--test2.2--test2.3;ID=query_1;Name=test1.1 chr1 S-MART test1.2 70 850 781 + . nbOverlaps=6;overlapsWith=test2.1--test2.2--test2.3--test2.4--test2.5--test2.6;ID=query_2;Name=test1.2 chr1 S-MART test1.3 550 850 201 + . nbOverlaps=4;overlapsWith=test2.1--test2.3--test2.5--test2.6;ID=query_3;Name=test1.3 chr1 S-MART test1.4 925 1025 101 + . nbOverlaps=2;overlapsWith=test2.1--test2.5;ID=query_4;Name=test1.4 chr1 S-MART test1.5 1201 1210 10 + . nbOverlaps=1;overlapsWith=test2.7;ID=query_5;Name=test1.5 """) f.close() def _writeExpOutFile_cas_1(self, fileName): f = open(fileName, 'w') f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;OverlapWith=query_3;score=1001;feature=test2.1;ID=test2.1\n") f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;OverlapWith=query_3;score=501;feature=test2.3;ID=test2.3\n") f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;OverlapWith=query_3;score=251;feature=test2.5;ID=test2.5\n") f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;OverlapWith=query_3;score=101;feature=test2.6;ID=test2.6\n") f.close() def _writeExpOutFile_cas_2(self, fileName): f = open(fileName, 'w') f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;OverlapWith=query_2;score=1001;feature=test2.1;ID=test2.1\n") f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tName=test2.2;OverlapWith=query_2;score=301;feature=test2.2;ID=test2.2\n") f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;OverlapWith=query_2;score=501;feature=test2.3;ID=test2.3\n") f.write("chr1\tS-MART\ttest2.4\t200\t450\t251\t+\t.\tName=test2.4;OverlapWith=query_2;score=251;feature=test2.4;ID=test2.4\n") f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;OverlapWith=query_2;score=251;feature=test2.5;ID=test2.5\n") f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;OverlapWith=query_2;score=101;feature=test2.6;ID=test2.6\n") f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;OverlapWith=query_3;score=1001;feature=test2.1;ID=test2.1\n") f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;OverlapWith=query_3;score=501;feature=test2.3;ID=test2.3\n") f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;OverlapWith=query_3;score=251;feature=test2.5;ID=test2.5\n") f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;OverlapWith=query_3;score=101;feature=test2.6;ID=test2.6\n") f.close() def _writeExpOutFile_all_overlap(self, fileName): f = open(fileName, 'w') f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;OverlapWith=query_2;score=1001;feature=test2.1;ID=test2.1\n") f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tName=test2.2;OverlapWith=query_2;score=301;feature=test2.2;ID=test2.2\n") f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;OverlapWith=query_2;score=501;feature=test2.3;ID=test2.3\n") f.write("chr1\tS-MART\ttest2.4\t200\t450\t251\t+\t.\tName=test2.4;OverlapWith=query_2;score=251;feature=test2.4;ID=test2.4\n") f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;OverlapWith=query_2;score=251;feature=test2.5;ID=test2.5\n") f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;OverlapWith=query_2;score=101;feature=test2.6;ID=test2.6\n") f.close() def _writeExpOutFile_overlap_to_children(self, fileName): f = open(fileName, 'w') f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;OverlapWith=query_3;score=1001;feature=test2.1;ID=test2.1\n") f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;OverlapWith=query_3;score=501;feature=test2.3;ID=test2.3\n") f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;OverlapWith=query_3;score=251;feature=test2.5;ID=test2.5\n") f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;OverlapWith=query_3;score=101;feature=test2.6;ID=test2.6\n") f.close() def _writeExpOutFile_not_overlap_to_children(self, fileName): f = open(fileName, 'w') f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;OverlapWith=query_1;score=1001;feature=test2.1;ID=test2.1\n") f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tName=test2.2;OverlapWith=query_1;score=301;feature=test2.2;ID=test2.2\n") f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;OverlapWith=query_1;score=501;feature=test2.3;ID=test2.3\n") f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;OverlapWith=query_4;score=1001;feature=test2.1;ID=test2.1\n") f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;OverlapWith=query_4;score=251;feature=test2.5;ID=test2.5\n") f.close() def _writeExpOutFile_no_overlap_right(self, fileName): f = open(fileName, 'w') f.close() def _writeExpOutFile_one_overlap(self, fileName): f = open(fileName, 'w') f.write("chr1\tS-MART\ttest2.7\t1200\t1300\t101\t+\t.\tName=test2.7;OverlapWith=query_5;score=101;feature=test2.7;ID=test2.7\n") f.close() def _writeQueryGff3File2(self, fileName): f = open(fileName, 'w') f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=query_1;Name=test1.1\n") f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=query_2;Name=test1.2\n") f.close() def _writeQueryGff3File(self, fileName): f = open(fileName, 'w') f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=query_1;Name=test1.1\n") f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=query_2;Name=test1.2\n") f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=query_3;Name=test1.3\n") f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=test1.4\n") f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=test1.5\n") f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=test1.6\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()