Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/Java/Python/ncList/test/MockFindOverlapsWithSeveralIntervals.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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1 from SMART.Java.Python.misc import Utils | |
2 | |
3 class MockFindOverlapsWithOneInterval (object) : | |
4 def write(self, inFileName): | |
5 Utils.writeFile(inFileName, "chr1\ttest\ttest1.1\t0\t1000\t.\t+\t.\tID=test1.1;Name=test1.1\n") | |
6 | |
7 class MockFindOverlapsWithServeralIntervals_case1 (object) : | |
8 def write(self,inFileName): | |
9 f = open(inFileName, "w") | |
10 f.write("chr1\ttest\ttest1.1\t0\t1000\t1001\t+\t.\tID=test1.1;Name=test1.1\n") | |
11 f.write("chr1\ttest\ttest1.2\t50\t350\t301\t+\t.\tID=test1.2;Name=test1.2\n") | |
12 f.write("chr1\ttest\ttest1.3\t100\t600\t501\t+\t.\tID=test1.3;Name=test1.3\n") | |
13 f.write("chr1\ttest\ttest1.4\t200\t450\t251\t+\t.\tID=test1.4;Name=test1.4\n") | |
14 f.write("chr1\ttest\ttest1.5\t700\t950\t251\t+\t.\tID=test1.5;Name=test1.5\n") | |
15 f.write("chr1\ttest\ttest1.6\t800\t900\t101\t+\t.\tID=test1.6;Name=test1.6\n") | |
16 f.write("chr1\ttest\ttest1.7\t1200\t1300\t101\t+\t.\tID=test1.7;Name=test1.7\n") | |
17 f.close() | |
18 | |
19 class MockFindOverlapsWithServeralIntervals_case2 (object) : | |
20 def write(self,inFileName): | |
21 f = open(inFileName,'w') | |
22 f.write("chr1\ttest\ttest2.1\t0\t500\t501\t+\t.\tID=test2.1;Name=test2.1\n") | |
23 f.write("chr1\ttest\ttest2.2\t50\t450\t401\t+\t.\tID=test2.2;Name=test2.2\n") | |
24 f.write("chr1\ttest\ttest2.3\t100\t400\t301\t+\t.\tID=test2.3;Name=test2.3\n") | |
25 f.write("chr1\ttest\ttest2.4\t100\t200\t101\t+\t.\tID=test2.4;Name=test2.4\n") | |
26 f.write("chr1\ttest\ttest2.5\t900\t1200\t301\t+\t.\tID=test2.5;Name=test2.5\n") | |
27 f.close() | |
28 | |
29 class MockFindOverlapsWithServeralIntervals_case3 (object) : | |
30 def write(self,inFileName): | |
31 f = open(inFileName,'w') | |
32 f.write("chr1\ttest\ttest3.1\t0\t500\t501\t+\t.\tID=test3.1;Name=test3.1\n") | |
33 f.write("chr1\ttest\ttest3.2\t50\t450\t401\t+\t.\tID=test3.2;Name=test3.2\n") | |
34 f.write("chr1\ttest\ttest3.3\t100\t400\t301\t+\t.\tID=test3.3;Name=test3.3\n") | |
35 f.write("chr1\ttest\ttest3.4\t100\t200\t101\t+\t.\tID=test3.4;Name=test3.4\n") | |
36 f.write("chr1\ttest\ttest3.5\t300\t400\t101\t+\t.\tID=test3.5;Name=test3.5\n") | |
37 f.write("chr1\ttest\ttest3.6\t800\t1000\t201\t+\t.\tID=test3.6;Name=test3.6\n") | |
38 f.close() | |
39 | |
40 class MockFindOverlapsWithServeralIntervals_case4_5 (object) : | |
41 def write(self,inFileName): | |
42 f = open(inFileName,'w') | |
43 f.write("chr1\ttest\ttest4.1\t0\t1000\t1001\t+\t.\tID=test4.1;Name=test4.1\n") | |
44 f.write("chr1\ttest\ttest4.2\t200\t800\t601\t+\t.\tID=test4.2;Name=test4.2\n") | |
45 f.write("chr1\ttest\ttest4.3\t400\t600\t201\t+\t.\tID=test4.3;Name=test4.3\n") | |
46 f.close() | |
47 | |
48 class MockFindOverlapsWithServeralIntervals_case6_7 (object) : | |
49 def write(self,inFileName): | |
50 f = open(inFileName,'w') | |
51 f.write("chr1\ttest\ttest6.1\t0\t1000\t1001\t+\t.\tID=test6.1;Name=test6.1\n") | |
52 f.write("chr1\ttest\ttest6.2\t100\t300\t201\t+\t.\tID=test6.2;Name=test6.2\n") | |
53 f.write("chr1\ttest\ttest6.3\t400\t500\t101\t+\t.\tID=test6.3;Name=test6.3\n") | |
54 f.write("chr1\ttest\ttest6.4\t510\t520\t11\t+\t.\tID=test6.4;Name=test6.4\n") | |
55 f.write("chr1\ttest\ttest6.5\t850\t950\t001\t+\t.\tID=test6.5;Name=test6.5\n") | |
56 f.close() | |
57 | |
58 class MockFindOverlapsWithServeralIntervals_case8 (object) : | |
59 def write(self,inFileName): | |
60 f = open(inFileName,'w') | |
61 f.write("chr1\ttest\ttest8.1\t0\t1000\t1001\t+\t.\tID=test8.1;Name=test8.1\n") | |
62 f.write("chr1\ttest\ttest8.2\t100\t200\t101\t+\t.\tID=test8.2;Name=test8.2\n") | |
63 f.write("chr1\ttest\ttest8.3\t300\t400\t101\t+\t.\tID=test8.3;Name=test8.3\n") | |
64 f.close() | |
65 | |
66 class MockFindOverlapsWithServeralIntervals_case9 (object) : | |
67 def write(self,inFileName): | |
68 f = open(inFileName,'w') | |
69 f.write("chr1\ttest\ttest9.1\t0\t1000\t1001\t+\t.\tID=test9.1;Name=test9.1\n") | |
70 f.write("chr1\ttest\ttest9.2\t600\t700\t101\t+\t.\tID=test9.2;Name=test9.2\n") | |
71 f.write("chr1\ttest\ttest9.3\t800\t1200\t401\t+\t.\tID=test9.3;Name=test9.3\n") | |
72 f.close() | |
73 | |
74 class MockFindOverlapsWithServeralIntervals_case10 (object) : | |
75 def write(self,inFileName): | |
76 f = open(inFileName,'w') | |
77 f.write("chr1\ttest\ttest10.1\t0\t1000\t1001\t+\t.\tID=test10.1;Name=test10.1\n") | |
78 f.write("chr1\ttest\ttest10.2\t100\t200\t101\t+\t.\tID=test10.2;Name=test10.2\n") | |
79 f.write("chr1\ttest\ttest10.3\t300\t400\t101\t+\t.\tID=test10.3;Name=test10.3\n") | |
80 f.write("chr1\ttest\ttest10.4\t500\t600\t101\t+\t.\tID=test10.4;Name=test10.4\n") | |
81 f.write("chr1\ttest\ttest10.5\t1200\t1300\t101\t+\t.\tID=test10.5;Name=test10.5\n") | |
82 f.write("chr1\ttest\ttest10.6\t1400\t1500\t101\t+\t.\tID=test10.6;Name=test10.6\n") | |
83 f.close() | |
84 | |
85 class MockFindOverlapsWithServeralIntervals_case11 (object) : | |
86 def write(self,inFileName): | |
87 f = open(inFileName,'w') | |
88 f.write("chr1\ttest\ttest11.1\t0\t500\t501\t+\t.\tID=test11.1;Name=test11.1\n") | |
89 f.write("chr1\ttest\ttest11.2\t100\t200\t101\t+\t.\tID=test11.2;Name=test11.2\n") | |
90 f.write("chr1\ttest\ttest11.3\t300\t400\t101\t+\t.\tID=test11.3;Name=test11.3\n") | |
91 f.write("chr1\ttest\ttest11.4\t700\t900\t201\t+\t.\tID=test11.4;Name=test11.4\n") | |
92 f.write("chr1\ttest\ttest11.5\t710\t720\t11\t+\t.\tID=test11.5;Name=test11.5\n") | |
93 f.write("chr1\ttest\ttest11.6\t740\t750\t11\t+\t.\tID=test11.6;Name=test11.6\n") | |
94 f.close() | |
95 | |
96 class MockFindOverlapsWithServeralIntervals_case12 (object) : | |
97 def write(self,inFileName): | |
98 f = open(inFileName,'w') | |
99 f.write("chr1\ttest\ttest12.1\t0\t1400\t.\t+\t.\tID=test12.1;Name=test12.1\n") | |
100 f.write("chr1\ttest\ttest12.2\t300\t500\t.\t+\t.\tID=test12.2;Name=test12.2\n") | |
101 f.write("chr1\ttest\ttest12.3\t300\t500\t.\t+\t.\tID=test12.3;Name=test12.3\n") | |
102 f.write("chr1\ttest\ttest12.4\t800\t1100\t.\t+\t.\tID=test12.4;Name=test12.4\n") | |
103 f.write("chr1\ttest\ttest12.5\t1200\t1300\t.\t+\t.\tID=test12.5;Name=test12.5\n") | |
104 f.close() | |
105 | |
106 class MockFindOverlapsWithServeralIntervals_query_case1 (object): | |
107 def write(self, fileName): | |
108 f = open(fileName, 'w') | |
109 f.write("chr1\tquery\tquery1.1\t25\t150\t126\t+\t.\tID=query_1;Name=query1.1\n") | |
110 f.write("chr1\tquery\tquery1.2\t70\t850\t781\t+\t.\tID=query_2;Name=query1.2\n") | |
111 f.write("chr1\tquery\tquery1.3\t550\t850\t201\t+\t.\tID=query_3;Name=query1.3\n") | |
112 f.write("chr1\tquery\tquery1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=query1.4\n") | |
113 f.write("chr1\tquery\tquery1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=query1.5\n") | |
114 f.write("chr1\tquery\tquery1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=query1.6\n") | |
115 f.close() | |
116 | |
117 class MockFindOverlapsWithServeralIntervals_query_case2 (object): | |
118 def write(self, fileName): | |
119 f = open(fileName, 'w') | |
120 f.write("chr1\tquery\tquery2.1\t150\t300\t151\t+\t.\tID=query_1;Name=query2.1\n") | |
121 f.write("chr1\tquery\tquery2.2\t300\t450\t151\t+\t.\tID=query_2;Name=query2.2\n") | |
122 f.write("chr1\tquery\tquery2.3\t480\t800\t321\t+\t.\tID=query_3;Name=query2.3\n") | |
123 f.write("chr1\tquery\tquery2.4\t560\t800\t241\t+\t.\tID=query_4;Name=query2.4\n") | |
124 f.write("chr1\tquery\tquery2.5\t850\t1000\t151\t+\t.\tID=query_5;Name=query2.5\n") | |
125 f.close() | |
126 | |
127 class MockFindOverlapsWithServeralIntervals_query_case3 (object): | |
128 def write(self, fileName): | |
129 f = open(fileName, 'w') | |
130 f.write("chr1\tquery\tquery3.1\t150\t250\t101\t+\t.\tID=query_1;Name=query3.1\n") | |
131 f.write("chr1\tquery\tquery3.2\t380\t400\t21\t+\t.\tID=query_2;Name=query3.2\n") | |
132 f.write("chr1\tquery\tquery3.3\t480\t520\t41\t+\t.\tID=query_3;Name=query3.3\n") | |
133 f.write("chr1\tquery\tquery3.4\t510\t700\t191\t+\t.\tID=query_4;Name=query3.4\n") | |
134 f.write("chr1\tquery\tquery3.5\t900\t950\t41\t+\t.\tID=query_5;Name=query3.5\n") | |
135 f.close() | |
136 | |
137 class MockFindOverlapsWithServeralIntervals_query_case4 (object): | |
138 def write(self, fileName): | |
139 f = open(fileName, 'w') | |
140 f.write("chr1\tquery\tquery4.1\t400\t500\t101\t+\t.\tID=query_1;Name=query4.1\n") | |
141 f.write("chr1\tquery\tquery4.2\t450\t600\t151\t+\t.\tID=query_2;Name=query4.2\n") | |
142 f.write("chr1\tquery\tquery4.3\t700\t800\t101\t+\t.\tID=query_3;Name=query4.3\n") | |
143 f.close() | |
144 | |
145 class MockFindOverlapsWithServeralIntervals_query_case5 (object): | |
146 def write(self, fileName): | |
147 f = open(fileName, 'w') | |
148 f.write("chr1\tquery\tquery5.1\t850\t950\t101\t+\t.\tID=query_1;Name=query5.1\n") | |
149 f.close() | |
150 | |
151 class MockFindOverlapsWithServeralIntervals_query_case6 (object): | |
152 def write(self, fileName): | |
153 f = open(fileName, 'w') | |
154 f.write("chr1\tquery\tquery6.1\t200\t300\t101\t+\t.\tID=query_1;Name=query6.1\n") | |
155 f.write("chr1\tquery\tquery6.2\t800\t900\t101\t+\t.\tID=query_2;Name=query6.2\n") | |
156 f.close() | |
157 | |
158 class MockFindOverlapsWithServeralIntervals_query_case7 (object): | |
159 def write(self, fileName): | |
160 f = open(fileName, 'w') | |
161 f.write("chr1\tquery\tquery6.1\t530\t550\t21\t+\t.\tID=query_1;Name=query6.1\n") | |
162 f.write("chr1\tquery\tquery6.2\t600\t700\t101\t+\t.\tID=query_2;Name=query6.2\n") | |
163 f.write("chr1\tquery\tquery6.3\t650\t900\t251\t+\t.\tID=query_3;Name=query6.3\n") | |
164 f.close() | |
165 | |
166 class MockFindOverlapsWithServeralIntervals_query_case8 (object): | |
167 def write(self, fileName): | |
168 f = open(fileName, 'w') | |
169 f.write("chr1\tquery\tquery7.1\t500\t600\t101\t+\t.\tID=query_1;Name=query7.1\n") | |
170 f.write("chr1\tquery\tquery7.2\t700\t800\t101\t+\t.\tID=query_2;Name=query7.2\n") | |
171 f.write("chr1\tquery\tquery7.3\t900\t1100\t201\t+\t.\tID=query_3;Name=query7.3\n") | |
172 f.write("chr1\tquery\tquery7.4\t1200\t1300\t101\t+\t.\tID=query_4;Name=query7.4\n") | |
173 f.close() | |
174 | |
175 class MockFindOverlapsWithServeralIntervals_query_case9 (object): | |
176 def write(self, fileName): | |
177 f = open(fileName, 'w') | |
178 f.write("chr1\tquery\tquery8.1\t400\t400\t101\t+\t.\tID=query_1;Name=query8.1\n") | |
179 f.write("chr1\tquery\tquery8.2\t550\t650\t101\t+\t.\tID=query_2;Name=query8.2\n") | |
180 f.close() | |
181 | |
182 class MockFindOverlapsWithServeralIntervals_query_case10 (object): | |
183 def write(self, fileName): | |
184 f = open(fileName, 'w') | |
185 f.write("chr1\tquery\tquery10.1\t700\t800\t101\t+\t.\tID=query_1;Name=query10.1\n") | |
186 f.write("chr1\tquery\tquery10.2\t900\t1000\t101\t+\t.\tID=query_2;Name=query10.2\n") | |
187 f.write("chr1\tquery\tquery10.3\t1100\t1300\t201\t+\t.\tID=query_3;Name=query10.3\n") | |
188 f.close() | |
189 | |
190 class MockFindOverlapsWithServeralIntervals_query_case11 (object): | |
191 def write(self, fileName): | |
192 f = open(fileName, 'w') | |
193 f.write("chr1\tquery\tquery11.1\t420\t480\t61\t+\t.\tID=query_1;Name=query11.1\n") | |
194 f.write("chr1\tquery\tquery11.2\t450\t715\t266\t+\t.\tID=query_2;Name=query11.2\n") | |
195 f.close() | |
196 | |
197 |