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/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  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  
  4  <command interpreter="perl">
  5  	execute_dwt_cor_aVb_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
 24This 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. 
 25
 26The 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
 28The program has two input files obtained as follows:
 29
 30For 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
 32The program gives two output files:
 33
 34- The first output file is a TABULAR format file representing the coefficient correlations and p-values 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 coefficient correlations for that feature at every scale.
 36
 37-----
 38
 39.. class:: warningmark
 40
 41**Note**
 42
 43In 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
 49Counting 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		82			162			158			79				459
 53		111			196			154			75				459
 54		98			178			160			79				475
 55		113			201			170			113				436
 56		113			173			147			95				446
 57		107			150			155			84				436
 58		106			166			175			96				448
 59		113			176			135			106				514
 60		113			170			152			87				450
 61		95			152			167			93				467
 62		91			171			169			118				426
 63		84			139			160			100				459
 64		92			154			164			104				440
 65		100			145			154			98				472
 66		91			161			152			71				461
 67		117			164			139			97				463
 68
 69And 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		269			366			330			238				1129
 73		239			328			327			283				1188
 74		254			351			358			297				1151
 75		262			371			355			256				1107
 76		254			361			352			234				1192
 77		265			354			367			240				1182
 78		255			359			333			235				1217
 79		271			389			387			272				1241
 80		240			305			341			249				1159
 81		272			351			337			257				1169
 82		275			351			337			233				1158
 83		305			331			361			253				1172
 84		277			341			343			253				1113
 85		266			362			355			267				1162
 86		235			326			329			241				1230
 87		254			335			360			251				1172
 88
 89  
 90We 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:
 91
 92The first output file::
 93
 94	motif1				motif2				1_cor		1_pval		2_cor		2_pval		3_cor		3_pval		4_cor		4_pval
 95	
 96	deletionHoptspot		insertionHoptspot		-0.1		0.346		-0.214		0.338		1		0.127		1		0.467
 97	deletionHoptspot		dnaPolPauseFrameshift		0.167		0.267		-0.214		0.334		1		0.122		1		0.511
 98	deletionHoptspot		topoisomeraseCleavageSite	0.167		0.277		0.143		0.412		-0.667		0.243		1		0.521
 99	deletionHoptspot		translinTarget			0		0.505		0.0714		0.441		1		0.124		1		0.518
100	insertionHoptspot		dnaPolPauseFrameshift		-0.202		0.238		0.143		0.379		-1		0.122		1		0.517
101	insertionHoptspot		topoisomeraseCleavageSite	-0.0336		0.457		0.214		0.29		0.667		0.252		1		0.503
102	insertionHoptspot		translinTarget			0.0672		0.389		0.429		0.186		-1		0.119		1		0.506
103	dnaPolPauseFrameshift		topoisomeraseCleavageSite	-0.353		0.101		0.357		0.228		0		0.612		-1		0.49
104	dnaPolPauseFrameshift		translinTarget			-0.151		0.303		-0.571		0.09		-0.333		0.37		-1		1
105	topoisomeraseCleavageSite	translinTarget			-0.37		0.077		-0.222		0.297		0.667		0.234		-1		0.471
106
107The second output file:
108
109.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_1.png
110.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_2.png
111.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_3.png
112.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_4.png
113.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_5.png
114.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_6.png
115.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_7.png
116.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_8.png
117.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_9.png
118.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_10.png
119
120
121  </help>  
122  
123</tool>