Mercurial > repos > yufei-luo > s_mart

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

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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