Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/ncList/test/Test_F_FindOverlapsWithOneInterval.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
---|---|
date | Fri, 18 Jan 2013 04:54:14 -0500 |
parents | |
children |
line wrap: on
line source
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()