Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/test/Test_F_selectByTag.py @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
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import unittest import os from SMART.Java.Python.misc import Utils class Test_F_selectByTag(unittest.TestCase): def setUp(self): self._inputFileName = "%s/SMART/Java/Python/TestFiles/inputMSWC1.gff3" % os.environ["REPET_PATH"] self._outputFileName = "outputSBT.gff3" self._expOutputFileName = "expSBT.gff3" def tearDown(self): os.remove(self._outputFileName) os.remove(self._expOutputFileName) def test_run_compulsory_option(self): cmd = 'python ../SelectByTag.py -i %s -f gff3 -g occurrence -o %s -v 0' % (self._inputFileName, self._outputFileName) os.system(cmd) self._writeExpDefault(self._expOutputFileName) self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName)) def test_run_value_option(self): cmd = 'python ../SelectByTag.py -i %s -f gff3 -a 1 -g occurrence -o %s -v 0' % (self._inputFileName, self._outputFileName) os.system(cmd) self._writeExpValueOption(self._expOutputFileName) self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName)) def test_run_min_option(self): cmd = 'python ../SelectByTag.py -i %s -f gff3 -m 3 -g occurrence -o %s -v 0' % (self._inputFileName, self._outputFileName) os.system(cmd) self._writeExpMinOption(self._expOutputFileName) self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName)) def test_run_max_option(self): cmd = 'python ../SelectByTag.py -i %s -f gff3 -M 1 -g occurrence -o %s -v 0' % (self._inputFileName, self._outputFileName) os.system(cmd) self._writeExpMaxOption(self._expOutputFileName) self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName)) def test_run_max_min_option(self): cmd = 'python ../SelectByTag.py -i %s -f gff3 -M 2 -m 1 -g occurrence -o %s -v 0' % (self._inputFileName, self._outputFileName) os.system(cmd) self._writeExpMaxMinOption(self._expOutputFileName) self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName)) def _writeExpDefault(self, fileName): f = open(fileName, 'w') f.write("""chr1 S-MART match 6155418 6155441 24 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1 chr2 S-MART match 26303950 26303981 32 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1 chr3 S-MART match 28320540 28320574 35 + . occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1 chr4 S-MART match 28565007 28565041 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1 chr6 S-MART match 48565007 48565041 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80;Name=test2/1 """) f.close() def _writeExpValueOption(self, fileName): f = open(fileName, 'w') f.write("""chr1 S-MART match 6155418 6155441 24 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1 chr2 S-MART match 26303950 26303981 32 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1 """) f.close() def _writeExpMinOption(self, fileName): f = open(fileName, 'w') f.write("""chr4 S-MART match 28565007 28565041 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1 chr6 S-MART match 48565007 48565041 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80;Name=test2/1 """) f.close() def _writeExpMaxOption(self, fileName): f = open(fileName, 'w') f.write("""chr1 S-MART match 6155418 6155441 24 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1 chr2 S-MART match 26303950 26303981 32 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1 """) f.close() def _writeExpMaxMinOption(self, fileName): f = open(fileName, 'w') f.write("""chr1 S-MART match 6155418 6155441 24 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1 chr2 S-MART match 26303950 26303981 32 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1 chr3 S-MART match 28320540 28320574 35 + . occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1 """) f.close() if __name__ == "__main__": unittest.main()