Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/ncList/test/Test_F_FindOverlapsWithSeveralIntervals.py @ 6:769e306b7933

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Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 import unittest
2 import os, os.path
3 from SMART.Java.Python.ncList.FindOverlapsWithSeveralIntervals import FindOverlapsWithSeveralIntervals
4 from SMART.Java.Python.misc import Utils
5
6 class Test_F_FindOverlapsWithSeveralIntervals(unittest.TestCase):
7
8 def setUp(self):
9 self._inputRefGff3FileName = 'sorted_Ref.gff3'
10 self._inputQueryGff3FileName = 'sorted_Query.gff3'
11 self._outputGff3FileName = 'output.gff3'
12 self._expOutputFileName = 'expOutGff3.gff3'
13 self._writeQueryGff3File(self._inputQueryGff3FileName)
14 self._writeGFF3File(self._inputRefGff3FileName)
15 self._iFOWSI = FindOverlapsWithSeveralIntervals(0)
16 self._iFOWSI.setRefFileName(self._inputRefGff3FileName, "gff3")
17 self._iFOWSI.setQueryFileName(self._inputQueryGff3FileName, "gff3")
18 self._iFOWSI.setOutputFileName(self._outputGff3FileName)
19 self._iFOWSI.prepareIntermediateFiles()
20 self._iFOWSI.createNCLists()
21
22 def tearDown(self):
23 for fileName in (self._inputRefGff3FileName, self._inputQueryGff3FileName, self._outputGff3FileName, self._expOutputFileName):
24 if os.path.exists(fileName):
25 os.remove(fileName)
26
27 def test_run_general(self):
28 self._writeQueryGff3File(self._inputQueryGff3FileName)
29 self._writeGFF3File(self._inputRefGff3FileName)
30 self._iFOWSI = FindOverlapsWithSeveralIntervals(0)
31 self._iFOWSI.setRefFileName(self._inputRefGff3FileName, "gff3")
32 self._iFOWSI.setQueryFileName(self._inputQueryGff3FileName, "gff3")
33 self._iFOWSI.setOutputFileName(self._outputGff3FileName)
34 self._iFOWSI.prepareIntermediateFiles()
35 self._iFOWSI.createNCLists()
36 self._iFOWSI.compare()
37 self._iFOWSI.close()
38 self._writeExpOutFile_general(self._expOutputFileName)
39 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
40
41 def test_run_general_asScript(self):
42 cmd = 'python ../FindOverlapsWithSeveralIntervals.py -i %s -f gff3 -j %s -g gff3 -o %s -v 0' % (self._inputQueryGff3FileName, self._inputRefGff3FileName, self._outputGff3FileName)
43 os.system(cmd)
44 self._writeExpOutFile_general(self._expOutputFileName)
45 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
46
47
48 def test_run_overlap_special_case(self):
49 inputQueryGff3FileName = 'query2.gff3'
50 self._writeQueryGff3File2(inputQueryGff3FileName)
51 self._iFOWSI = FindOverlapsWithSeveralIntervals(0)
52 self._iFOWSI.setRefFileName(self._inputRefGff3FileName, "gff3")
53 self._iFOWSI.setQueryFileName(inputQueryGff3FileName, "gff3")
54 self._iFOWSI.setOutputFileName(self._outputGff3FileName)
55 self._iFOWSI.prepareIntermediateFiles()
56 self._iFOWSI.createNCLists()
57 self._iFOWSI.compare()
58 self._iFOWSI.close()
59 self._writeExpOutFile_special_case(self._expOutputFileName)
60 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
61 os.remove(inputQueryGff3FileName)
62
63 def test_run_overlap_special_case_asScript(self):
64 inputQueryGff3FileName = 'query2.gff3'
65 self._writeQueryGff3File2(inputQueryGff3FileName)
66 cmd = 'python ../FindOverlapsWithSeveralIntervals.py -i %s -f gff3 -j %s -g gff3 -o %s -v 0' % (inputQueryGff3FileName, self._inputRefGff3FileName, self._outputGff3FileName)
67 os.system(cmd)
68 self._writeExpOutFile_special_case(self._expOutputFileName)
69 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
70 os.remove(inputQueryGff3FileName)
71
72 def _writeExpOutFile_special_case(self, fileName):
73 f = open(fileName, 'w')
74 f.write("chr1 S-MART test2 1250 1300 781 + . nbOverlaps=1;overlapsWith=test2.7;ID=query_2;Name=test1.2\n")
75 f.close()
76
77 def _writeExpOutFile_general(self, fileName):
78 f = open(fileName, 'w')
79 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
80 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
81 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
82 chr1 S-MART test1.4 925 1025 101 + . nbOverlaps=2;overlapsWith=test2.1--test2.5;ID=query_4;Name=test1.4
83 chr1 S-MART test1.5 1201 1210 10 + . nbOverlaps=1;overlapsWith=test2.7;ID=query_5;Name=test1.5
84 """)
85 f.close()
86
87 def _writeExpOutFile_cas_1(self, fileName):
88 f = open(fileName, 'w')
89 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")
90 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")
91 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")
92 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")
93 f.close()
94
95 def _writeExpOutFile_cas_2(self, fileName):
96 f = open(fileName, 'w')
97 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")
98 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")
99 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")
100 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")
101 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")
102 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")
103 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")
104 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")
105 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")
106 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")
107 f.close()
108
109 def _writeExpOutFile_all_overlap(self, fileName):
110 f = open(fileName, 'w')
111 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")
112 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")
113 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")
114 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")
115 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")
116 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")
117 f.close()
118
119 def _writeExpOutFile_overlap_to_children(self, fileName):
120 f = open(fileName, 'w')
121 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")
122 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")
123 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")
124 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")
125 f.close()
126
127 def _writeExpOutFile_not_overlap_to_children(self, fileName):
128 f = open(fileName, 'w')
129 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")
130 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")
131 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")
132 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")
133 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")
134 f.close()
135
136 def _writeExpOutFile_no_overlap_right(self, fileName):
137 f = open(fileName, 'w')
138 f.close()
139
140 def _writeExpOutFile_one_overlap(self, fileName):
141 f = open(fileName, 'w')
142 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")
143 f.close()
144
145 def _writeQueryGff3File2(self, fileName):
146 f = open(fileName, 'w')
147 f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=query_1;Name=test1.1\n")
148 f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=query_2;Name=test1.2\n")
149 f.close()
150
151 def _writeQueryGff3File(self, fileName):
152 f = open(fileName, 'w')
153 f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=query_1;Name=test1.1\n")
154 f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=query_2;Name=test1.2\n")
155 f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=query_3;Name=test1.3\n")
156 f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=test1.4\n")
157 f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=test1.5\n")
158 f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=test1.6\n")
159 f.close()
160
161 def _writeGFF3File(self, fileName):
162 f = open(fileName, "w")
163 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n")
164 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n")
165 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n")
166 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n")
167 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n")
168 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n")
169 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n")
170 f.close()
171
172 if __name__ == "__main__":
173 unittest.main()