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comparison tools/discreteWavelet/execute_dwt_IvC_all.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" name="Compute P-values and Second Moments for Feature Occurrences" version="1.0.0">
2 <description>between two datasets using Discrete Wavelet Transfoms</description>
3
4 <command interpreter="perl">
5 execute_dwt_IvC_all.pl $inputFile1 $inputFile2 $outputFile1 $outputFile2
6 </command>
7
8 <inputs>
9 <param format="tabular" name="inputFile1" type="data" label="Select the first input file"/>
10 <param format="tabular" name="inputFile2" type="data" label="Select the second input file"/>
11 </inputs>
12
13 <outputs>
14 <data format="tabular" name="outputFile1"/>
15 <data format="pdf" name="outputFile2"/>
16 </outputs>
17
18 <help>
19
20 .. class:: infomark
21
22 **What it does**
23
24 This program generates plots and computes table matrix of second moments, p-values, and test orientations at multiple scales for the correlation between the occurrences of features in one dataset and their occurrences in another using multiscale wavelet analysis technique.
25
26 The program assumes that the user has two sets of DNA sequences, S1 and S1, each of which consists of one or more sequences of equal length. Each sequence in each set is divided into the same number of multiple intervals n such that n = 2^k, where k is a positive integer and k >= 1. Thus, n could be any value of the set {2, 4, 8, 16, 32, 64, 128, ...}. k represents the number of scales.
27
28 The program has two input files obtained as follows:
29
30 For a given set of features, say motifs, the user counts the number of occurrences of each feature in each interval of each sequence in S1 and S1, and builds two tabular files representing the count results in each interval of S1 and S1. These are the input files of the program.
31
32 The program gives two output files:
33
34 - The first output file is a TABULAR format file representing the second moments, p-values, and test orientations for each feature at each scale.
35 - The second output file is a PDF file consisting of as many figures as the number of features, such that each figure represents the values of the second moment for that feature at every scale.
36
37 -----
38
39 .. class:: warningmark
40
41 **Note**
42
43 In order to obtain empirical p-values, a random perumtation test is implemented by the program, which results in the fact that the program gives slightly different results each time it is run on the same input file.
44
45 -----
46
47 **Example**
48
49 Counting the occurrences of 5 features (motifs) in 16 intervals (one line per interval) of the DNA sequences in S1 gives the following tabular file::
50
51 deletionHoptspot insertionHoptspot dnaPolPauseFrameshift topoisomeraseCleavageSite translinTarget
52 226 403 416 221 1165
53 236 444 380 241 1223
54 242 496 391 195 1116
55 243 429 364 191 1118
56 244 410 371 236 1063
57 230 386 370 217 1087
58 275 404 402 214 1044
59 265 443 365 231 1086
60 255 390 354 246 1114
61 281 384 406 232 1102
62 263 459 369 251 1135
63 280 433 400 251 1159
64 278 385 382 231 1147
65 248 393 389 211 1162
66 251 403 385 246 1114
67 239 383 347 227 1172
68
69 And counting the occurrences of 5 features (motifs) in 16 intervals (one line per interval) of the DNA sequences in S2 gives the following tabular file::
70
71 deletionHoptspot insertionHoptspot dnaPolPauseFrameshift topoisomeraseCleavageSite translinTarget
72 235 374 407 257 1159
73 244 356 353 212 1128
74 233 343 322 204 1110
75 222 329 398 253 1054
76 216 325 328 253 1129
77 257 368 352 221 1115
78 238 360 346 224 1102
79 225 350 377 248 1107
80 230 330 365 236 1132
81 241 389 357 220 1120
82 274 354 392 235 1120
83 250 379 354 210 1102
84 254 329 320 251 1080
85 221 355 406 279 1127
86 224 330 390 249 1129
87 246 366 364 218 1176
88
89
90 We notice that the number of scales here is 4 because 16 = 2^4. Runnig the program on the above input files gives the following output:
91
92 The first output file::
93
94 motif 1_moment2 1_pval 1_test 2_moment2 2_pval 2_test 3_moment2 3_pval 3_test 4_moment2 4_pval 4_test
95
96 deletionHoptspot 0.8751 0.376 L 1.549 0.168 R 0.6152 0.434 L 0.5735 0.488 R
97 insertionHoptspot 0.902 0.396 L 1.172 0.332 R 0.6843 0.456 L 1.728 0.213 R
98 dnaPolPauseFrameshift 1.65 0.013 R 0.267 0.055 L 0.1387 0.124 L 0.4516 0.498 L
99 topoisomeraseCleavageSite 0.7443 0.233 L 1.023 0.432 R 1.933 0.155 R 1.09 0.3 R
100 translinTarget 0.5084 0.057 L 0.8219 0.446 L 3.604 0.019 R 0.4377 0.492 L
101
102 The second output file:
103
104 .. image:: ./static/operation_icons/dwt_IvC_1.png
105 .. image:: ./static/operation_icons/dwt_IvC_2.png
106 .. image:: ./static/operation_icons/dwt_IvC_3.png
107 .. image:: ./static/operation_icons/dwt_IvC_4.png
108 .. image:: ./static/operation_icons/dwt_IvC_5.png
109
110 </help>
111
112 </tool>