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comparison smart_toolShed/SMART/Java/Python/ncList/test/Test_F_FindOverlapsWithOneInterval.py @ 0:e0f8dcca02ed

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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
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-1:000000000000 0:e0f8dcca02ed
1 import unittest
2 import struct
3 import os
4 from SMART.Java.Python.structure.Interval import Interval
5 from SMART.Java.Python.ncList.FindOverlapsWithOneInterval import FindOverlapsWithOneInterval
6 from SMART.Java.Python.misc import Utils
7
8 class Test_F_FindOverlapsWithOneInterval(unittest.TestCase):
9
10 def setUp(self):
11 self._inputGff3FileName = 'sortedFile.gff3'
12 self._writeGFF3File(self._inputGff3FileName)
13 self._obsFileName = "overlap.gff3"
14 self._expFileName = "expFile.gff3"
15 self._iFOWOI = FindOverlapsWithOneInterval(0)
16 self._iFOWOI.setFileName(self._inputGff3FileName, "gff3")
17 self._iFOWOI.setOutputFileName(self._obsFileName)
18
19 def tearDown(self):
20 os.remove(self._inputGff3FileName)
21 os.remove(self._obsFileName)
22 os.remove(self._expFileName)
23
24 def test_run_general(self):
25 self._iFOWOI.setInterval("chr1", 500, 850)
26 self._iFOWOI.run()
27 self._writeExpGFF3File_general(self._expFileName)
28 self.assertTrue(Utils.diff(self._expFileName, self._obsFileName))
29
30 # def test_run_general_asScript(self):
31 # cmd = 'python ../FindOverlapsWithOneInterval.py -i %s -f gff3 -o %s -c chr1 -s 500 -e 850 -v 0' % (self._inputGff3FileName, self._obsFileName)
32 # os.system(cmd)
33 # self._writeExpGFF3File_general(self._expFileName)
34 # self.assertTrue(Utils.diff(self._expFileName, self._obsFileName))
35 #
36 # def test_run_one_overlap(self):
37 # self._iFOWOI.setInterval("chr1", 1250, 1450)
38 # self._iFOWOI.run()
39 # self._writeExpGFF3File_one_overlap(self._expFileName)
40 # self.assertTrue(Utils.diff(self._expFileName, self._obsFileName))
41 #
42 # def test_run_one_overlap_asScript(self):
43 # cmd = 'python ../FindOverlapsWithOneInterval.py -i %s -f gff3 -o %s -c chr1 -s 1250 -e 1450 -v 0' % (self._inputGff3FileName, self._obsFileName)
44 # os.system(cmd)
45 # self._writeExpGFF3File_one_overlap(self._expFileName)
46 # self.assertTrue(Utils.diff(self._expFileName, self._obsFileName))
47 #
48 # def test_run_all_overlap(self):
49 # self._iFOWOI.setInterval("chr1", 300, 1250)
50 # self._iFOWOI.run()
51 # self._writeExpGff3File_all_overlap(self._expFileName)
52 # self.assertTrue(Utils.diff(self._expFileName, self._obsFileName))
53 #
54 # def test_run_all_overlap_asScript(self):
55 # cmd = 'python ../FindOverlapsWithOneInterval.py -i %s -f gff3 -o %s -c chr1 -s 300 -e 1250 -v 0' % (self._inputGff3FileName, self._obsFileName)
56 # os.system(cmd)
57 # self._writeExpGff3File_all_overlap(self._expFileName)
58 # self.assertTrue(Utils.diff(self._expFileName, self._obsFileName))
59 #
60 # def test_run_no_overlap_right(self):
61 # self._iFOWOI.setInterval("chr1", 1400, 1500)
62 # self._iFOWOI.run()
63 # f = open(self._expFileName, "w")
64 # f.close()
65 # self.assertTrue(Utils.diff(self._expFileName, self._obsFileName))
66 #
67 # def test_run_no_overlap_right_asScript(self):
68 # cmd = 'python ../FindOverlapsWithOneInterval.py -i %s -f gff3 -o %s -c chr1 -s 1400 -e 1500 -v 0' % (self._inputGff3FileName, self._obsFileName)
69 # os.system(cmd)
70 # f = open(self._expFileName, "w")
71 # f.close()
72 # self.assertTrue(Utils.diff(self._expFileName, self._obsFileName))
73 #
74 # def test_run_no_overlap_left(self):
75 # self._iFOWOI.setInterval("chr1", 0, 8)
76 # self._iFOWOI.run()
77 # f = open(self._expFileName, "w")
78 # f.close()
79 # self.assertTrue(Utils.diff(self._expFileName, self._obsFileName))
80 #
81 # def test_run_no_overlap_left_asScript(self):
82 # cmd = 'python ../FindOverlapsWithOneInterval.py -i %s -f gff3 -o %s -c chr1 -s 0 -e 8 -v 0' % (self._inputGff3FileName, self._obsFileName)
83 # os.system(cmd)
84 # f = open(self._expFileName, "w")
85 # f.close()
86 # self.assertTrue(Utils.diff(self._expFileName, self._obsFileName))
87
88 def _writeExpGff3File_all_overlap(self, fileName):
89 f = open(fileName, 'w')
90 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n")
91 f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n")
92 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n")
93 f.write("chr1\tS-MART\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n")
94 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n")
95 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n")
96 f.write("chr1\tS-MART\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n")
97 f.close()
98
99 def _writeExpGFF3File_one_overlap(self, fileName):
100 f = open(fileName, "w")
101 f.write("chr1\tS-MART\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n")
102 f.close()
103
104 def _writeExpGFF3File_general(self, fileName):
105 f = open(fileName, "w")
106 f.write("chr1\tS-MART\ttranscript\t500\t850\t.\t+\t.\tnbOverlaps=4;overlapsWith=test2.1--test2.3--test2.5--test2.6\n")
107 f.close()
108
109 def _writeGFF3File(self, fileName):
110 f = open(fileName, "w")
111 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n")
112 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n")
113 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n")
114 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n")
115 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n")
116 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n")
117 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n")
118 f.close()
119
120 if __name__ == "__main__":
121 unittest.main()