/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 123 lines · 91 code · 32 blank · 0 comment · 0 complexity · 4d799a4b4d6e542ec2e53e0db9c9b1c2 MD5 · raw file

  1. <tool id="compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom" name="Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features" version="1.0.0">
  2. <description>between two datasets using Discrete Wavelet Transfoms</description>
  3. <command interpreter="perl">
  4. execute_dwt_cor_aVb_all.pl $inputFile1 $inputFile2 $outputFile1 $outputFile2
  5. </command>
  6. <inputs>
  7. <param format="tabular" name="inputFile1" type="data" label="Select the first input file"/>
  8. <param format="tabular" name="inputFile2" type="data" label="Select the second input file"/>
  9. </inputs>
  10. <outputs>
  11. <data format="tabular" name="outputFile1"/>
  12. <data format="pdf" name="outputFile2"/>
  13. </outputs>
  14. <help>
  15. .. class:: infomark
  16. **What it does**
  17. This program generates plots and computes table matrix of coefficient correlations and p-values at multiple scales for the correlation between the occurrences of features in one dataset and their occurrences in another using multiscale wavelet analysis technique.
  18. 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.
  19. The program has two input files obtained as follows:
  20. 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.
  21. The program gives two output files:
  22. - The first output file is a TABULAR format file representing the coefficient correlations and p-values for each feature at each scale.
  23. - 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 coefficient correlations for that feature at every scale.
  24. -----
  25. .. class:: warningmark
  26. **Note**
  27. 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.
  28. -----
  29. **Example**
  30. 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::
  31. deletionHoptspot insertionHoptspot dnaPolPauseFrameshift topoisomeraseCleavageSite translinTarget
  32. 82 162 158 79 459
  33. 111 196 154 75 459
  34. 98 178 160 79 475
  35. 113 201 170 113 436
  36. 113 173 147 95 446
  37. 107 150 155 84 436
  38. 106 166 175 96 448
  39. 113 176 135 106 514
  40. 113 170 152 87 450
  41. 95 152 167 93 467
  42. 91 171 169 118 426
  43. 84 139 160 100 459
  44. 92 154 164 104 440
  45. 100 145 154 98 472
  46. 91 161 152 71 461
  47. 117 164 139 97 463
  48. 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::
  49. deletionHoptspot insertionHoptspot dnaPolPauseFrameshift topoisomeraseCleavageSite translinTarget
  50. 269 366 330 238 1129
  51. 239 328 327 283 1188
  52. 254 351 358 297 1151
  53. 262 371 355 256 1107
  54. 254 361 352 234 1192
  55. 265 354 367 240 1182
  56. 255 359 333 235 1217
  57. 271 389 387 272 1241
  58. 240 305 341 249 1159
  59. 272 351 337 257 1169
  60. 275 351 337 233 1158
  61. 305 331 361 253 1172
  62. 277 341 343 253 1113
  63. 266 362 355 267 1162
  64. 235 326 329 241 1230
  65. 254 335 360 251 1172
  66. We notice that the number of scales here is 4 because 16 = 2^4. Running the program on the above input files gives the following output:
  67. The first output file::
  68. motif1 motif2 1_cor 1_pval 2_cor 2_pval 3_cor 3_pval 4_cor 4_pval
  69. deletionHoptspot insertionHoptspot -0.1 0.346 -0.214 0.338 1 0.127 1 0.467
  70. deletionHoptspot dnaPolPauseFrameshift 0.167 0.267 -0.214 0.334 1 0.122 1 0.511
  71. deletionHoptspot topoisomeraseCleavageSite 0.167 0.277 0.143 0.412 -0.667 0.243 1 0.521
  72. deletionHoptspot translinTarget 0 0.505 0.0714 0.441 1 0.124 1 0.518
  73. insertionHoptspot dnaPolPauseFrameshift -0.202 0.238 0.143 0.379 -1 0.122 1 0.517
  74. insertionHoptspot topoisomeraseCleavageSite -0.0336 0.457 0.214 0.29 0.667 0.252 1 0.503
  75. insertionHoptspot translinTarget 0.0672 0.389 0.429 0.186 -1 0.119 1 0.506
  76. dnaPolPauseFrameshift topoisomeraseCleavageSite -0.353 0.101 0.357 0.228 0 0.612 -1 0.49
  77. dnaPolPauseFrameshift translinTarget -0.151 0.303 -0.571 0.09 -0.333 0.37 -1 1
  78. topoisomeraseCleavageSite translinTarget -0.37 0.077 -0.222 0.297 0.667 0.234 -1 0.471
  79. The second output file:
  80. .. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_1.png
  81. .. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_2.png
  82. .. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_3.png
  83. .. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_4.png
  84. .. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_5.png
  85. .. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_6.png
  86. .. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_7.png
  87. .. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_8.png
  88. .. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_9.png
  89. .. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_10.png
  90. </help>
  91. </tool>