# HG changeset patch
# User devteam
# Date 1390498267 18000
# Node ID 27c5c2979e32380e8d8c70b15a000653311b7253

Imported from capsule None

diff -r 000000000000 -r 27c5c2979e32 execute_dwt_var_perClass.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/execute_dwt_var_perClass.pl	Thu Jan 23 12:31:07 2014 -0500
@@ -0,0 +1,320 @@
+#!/usr/bin/perl -w
+
+use warnings;
+use IO::Handle;
+use POSIX qw(floor ceil);
+
+# example: perl execute_dwt_var_perClass.pl hg18_NCNR_10bp_3flanks_deletionHotspot_data_del.txt deletionHotspot 3flanks del
+
+$usage = "execute_dwt_var_perClass.pl [TABULAR.in] [TABULAR.out] [TABULAR.out] [PDF.out] \n";
+die $usage unless @ARGV == 4;
+
+#get the input arguments
+my $inputFile = $ARGV[0];
+my $firstOutputFile = $ARGV[1];
+my $secondOutputFile = $ARGV[2];
+my $thirdOutputFile = $ARGV[3];
+
+open (INPUT, "<", $inputFile) || die("Could not open file $inputFile \n");
+open (OUTPUT1, ">", $firstOutputFile) || die("Could not open file $firstOutputFile \n");
+open (OUTPUT2, ">", $secondOutputFile) || die("Could not open file $secondOutputFile \n");
+open (OUTPUT3, ">", $thirdOutputFile) || die("Could not open file $thirdOutputFile \n");
+open (ERROR,  ">", "error.txt")  or die ("Could not open file error.txt \n");
+
+#save all error messages into the error file $errorFile using the error file handle ERROR
+STDERR -> fdopen( \*ERROR,  "w" ) or die ("Could not direct errors to the error file error.txt \n");
+
+# choosing meaningful names for the output files
+$max_dwt = $firstOutputFile; 
+$pvalue = $secondOutputFile; 
+$pdf = $thirdOutputFile; 
+
+# count the number of columns in the input file
+while($buffer = <INPUT>){
+	#if ($buffer =~ m/interval/){
+		chomp($buffer);
+		$buffer =~ s/^#\s*//;
+		@contrl = split(/\t/, $buffer);
+		last;
+	#}
+}
+print "The number of columns in the input file is: " . (@contrl) . "\n";
+print "\n";
+
+# count the number of motifs in the input file
+$count = 0;
+for ($i = 0; $i < @contrl; $i++){
+	$count++;
+	print "# $contrl[$i]\n";
+}
+print "The number of motifs in the input file is:  $count \n";
+
+# check if the number of motifs is not a multiple of 12, and round up is so
+$count2 = ($count/12);
+if ($count2 =~ m/(\D)/){
+	print "the number of motifs is not a multiple of 12 \n";
+	$count2 = ceil($count2);
+}
+else {
+	print "the number of motifs is a multiple of 12 \n";
+}
+print "There will be $count2 subfiles\n\n";
+
+# split infile into subfiles only 12 motif per file for R plotting
+for ($x = 1; $x <= $count2; $x++){
+	$a = (($x - 1) * 12 + 1);
+	$b = $x * 12;
+	
+	if ($x < $count2){
+		print "# data.short $x <- data_test[, +c($a:$b)]; \n"; 
+	}
+	else{
+		print "# data.short $x <- data_test[, +c($a:ncol(data_test)]; \n";
+	}
+}
+
+print "\n";
+print "There are 4 output files: \n";
+print "The first output file is a pdf file\n";
+print "The second output file is a max_dwt file\n";
+print "The third output file is a pvalues file\n";
+print "The fourth output file is a test_final_pvalues file\n";
+
+# write R script
+$r_script = "get_dwt_varPermut_getMax.r"; 
+print "The R file name is: $r_script \n";
+
+open(Rcmd, ">", "$r_script") or die "Cannot open $r_script \n\n";
+
+print Rcmd "
+	######################################################################
+	# plot power spectra, i.e. wavelet variance by class
+	# add code to create null bands by permuting the original data series
+	# get class of maximum significant variance per feature
+	# generate plots and table matrix of variance including p-values
+	######################################################################
+	library(\"Rwave\");
+	library(\"wavethresh\");
+	library(\"waveslim\");
+
+	options(echo = FALSE)
+
+	# normalize data
+	norm <- function(data){
+		v <- (data-mean(data))/sd(data);
+    	if(sum(is.na(v)) >= 1){
+    		v<-data;
+    	}
+    	return(v);
+	}
+
+	dwt_var_permut_getMax <- function(data, names, filter = 4, bc = \"symmetric\", method = \"kendall\", wf = \"haar\", boundary = \"reflection\") {
+		max_var = NULL;
+    	matrix = NULL;
+		title = NULL;
+    	final_pvalue = NULL;
+		short.levels = NULL;
+		scale = NULL;
+	
+    	print(names);
+    	
+   	 	par(mfcol = c(length(names), length(names)), mar = c(0, 0, 0, 0), oma = c(4, 3, 3, 2), xaxt = \"s\", cex = 1, las = 1);
+   	 	
+    	short.levels <- wd(data[, 1], filter.number = filter, bc = bc)\$nlevels;
+    	
+    	title <- c(\"motif\");
+    	for (i in 1:short.levels){
+    		title <- c(title, paste(i, \"var\", sep = \"_\"), paste(i, \"pval\", sep = \"_\"), paste(i, \"test\", sep = \"_\"));
+    	}
+    	print(title);
+        
+		# normalize the raw data
+    	data<-apply(data,2,norm);
+
+    	for(i in 1:length(names)){
+    		for(j in 1:length(names)){
+				temp = NULL;
+				results = NULL;
+				wave1.dwt = NULL;
+				out = NULL;
+				
+				out <- vector(length = length(title));
+            	temp <- vector(length = short.levels);
+            	
+            	if(i < j) {
+            		plot(temp, type = \"n\", axes = FALSE, xlab = NA, ylab = NA);
+                	box(col = \"grey\"); 
+                	grid(ny = 0, nx = NULL);
+            	} else {
+            		if (i > j){
+                		plot(temp, type = \"n\", axes = FALSE, xlab = NA, ylab = NA);
+                    	box(col = \"grey\"); 
+                    	grid(ny = 0, nx = NULL);
+                 	} else {
+                 	
+                 		wave1.dwt <- dwt(data[, i], wf = wf, short.levels, boundary = boundary); 
+                		
+                		temp_row = (short.levels + 1 ) * -1;
+                		temp_col = 1;
+                    	temp <- wave.variance(wave1.dwt)[temp_row, temp_col];
+
+                    	#permutations code :
+                    	feature1 = NULL;
+						null = NULL;
+						var_25 = NULL;
+						var_975 = NULL;
+						med = NULL;
+
+                    	feature1 = data[, i];
+                    	for (k in 1:1000) {
+							nk_1 = NULL;
+							null.levels = NULL;
+							var = NULL;
+							null_wave1 = NULL;
+
+                        	nk_1 = sample(feature1, length(feature1), replace = FALSE);
+                        	null.levels <- wd(nk_1, filter.number = filter, bc = bc)\$nlevels;
+                        	var <- vector(length = length(null.levels));
+                        	null_wave1 <- dwt(nk_1, wf = wf, short.levels, boundary = boundary);
+                        	var<- wave.variance(null_wave1)[-8, 1];
+                        	null= rbind(null, var);
+                    	}
+                    	null <- apply(null, 2, sort, na.last = TRUE);
+                    	var_25 <- null[25, ];
+                    	var_975 <- null[975, ];
+                    	med <- (apply(null, 2, median, na.rm = TRUE));
+
+                    	# plot
+                    	results <- cbind(temp, var_25, var_975);
+                    	matplot(results, type = \"b\", pch = \"*\", lty = 1, col = c(1, 2, 2), axes = F);
+
+                    	# get pvalues by comparison to null distribution
+                    	out <- (names[i]);
+                    	for (m in 1:length(temp)){
+                    		print(paste(\"scale\", m, sep = \" \"));
+                        	print(paste(\"var\", temp[m], sep = \" \"));
+                        	print(paste(\"med\", med[m], sep = \" \"));
+                        	pv = tail = NULL;
+							out <- c(out, format(temp[m], digits = 3));	
+                        	if (temp[m] >= med[m]){
+                        		# R tail test
+                            	print(\"R\");
+	                        	tail <- \"R\";
+                            	pv <- (length(which(null[, m] >= temp[m])))/(length(na.exclude(null[, m])));
+
+                        	} else {
+                        		if (temp[m] < med[m]){
+                                	# L tail test
+                                	print(\"L\");
+	                            	tail <- \"L\";
+                                	pv <- (length(which(null[, m] <= temp[m])))/(length(na.exclude(null[, m])));
+                        		}
+							}
+							out <- c(out, pv);
+							print(pv);
+							out <- c(out, tail);
+                    	}
+                    	final_pvalue <-rbind(final_pvalue, out);
+                 	
+                 
+                    	# get variances outside null bands by comparing temp to null
+                    	## temp stores variance for each scale, and null stores permuted variances for null bands
+                    	for (n in 1:length(temp)){
+                    		if (temp[n] <= var_975[n]){
+                        		temp[n] <- NA;
+                        	} else {
+                        		temp[n] <- temp[n];
+                        	}
+                    	}
+                    	matrix <- rbind(matrix, temp)
+            		}
+            	}
+	        	# labels
+	        	if (i == 1){
+	        		mtext(names[j], side = 2, line = 0.5, las = 3, cex = 0.25);
+	        	}
+	        	if (j == 1){
+	        		mtext(names[i], side = 3, line = 0.5, cex = 0.25);
+	        	}
+	        	if (j == length(names)){
+	        		axis(1, at = (1:short.levels), las = 3, cex.axis = 0.5);
+	        	}
+    		}
+    	}
+		colnames(final_pvalue) <- title;
+    	#write.table(final_pvalue, file = \"test_final_pvalue.txt\", sep = \"\\t\", quote = FALSE, row.names = FALSE, append = TRUE);
+
+		# get maximum variance larger than expectation by comparison to null bands
+    	varnames <- vector();
+    	for(i in 1:length(names)){
+    		name1 = paste(names[i], \"var\", sep = \"_\")
+        	varnames <- c(varnames, name1)
+    	}
+   		rownames(matrix) <- varnames;
+    	colnames(matrix) <- (1:short.levels);
+    	max_var <- names;
+    	scale <- vector(length = length(names));
+    	for (x in 1:nrow(matrix)){
+        	if (length(which.max(matrix[x, ])) == 0){
+            	scale[x] <- NA;
+        	}
+        	else{
+        		scale[x] <- colnames(matrix)[which.max(matrix[x, ])];
+        	}
+    	}
+    	max_var <- cbind(max_var, scale);
+    	write.table(max_var, file = \"$max_dwt\", sep = \"\\t\", quote = FALSE, row.names = FALSE, append = TRUE);
+    	return(final_pvalue);
+	}\n";
+
+print Rcmd "
+	# execute
+	# read in data 
+	
+	data_test = NULL;
+	data_test <- read.delim(\"$inputFile\");
+	
+	pdf(file = \"$pdf\", width = 11, height = 8);
+	
+	# loop to read and execute on all $count2 subfiles
+	final = NULL;
+	for (x in 1:$count2){
+		sub = NULL;
+		sub_names = NULL;
+		a = NULL;
+		b = NULL;
+		
+    	a = ((x - 1) * 12 + 1);
+    	b = x * 12;
+    
+    	if (x < $count2){
+    		sub <- data_test[, +c(a:b)];
+			sub_names <- colnames(data_test)[a:b];
+			final <- rbind(final, dwt_var_permut_getMax(sub, sub_names));
+    	}
+    	else{
+    		sub <- data_test[, +c(a:ncol(data_test))];
+			sub_names <- colnames(data_test)[a:ncol(data_test)];
+			final <- rbind(final, dwt_var_permut_getMax(sub, sub_names));
+			
+    	}
+	}
+
+	dev.off();
+
+	write.table(final, file = \"$pvalue\", sep = \"\\t\", quote = FALSE, row.names = FALSE);
+
+	#eof\n";
+
+close Rcmd;
+
+system("echo \"wavelet ANOVA started on \`hostname\` at \`date\`\"\n");
+system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
+system("echo \"wavelet ANOVA ended on \`hostname\` at \`date\`\"\n");
+
+#close the input and output and error files
+close(ERROR);
+close(OUTPUT3);
+close(OUTPUT2);
+close(OUTPUT1);
+close(INPUT);
\ No newline at end of file
diff -r 000000000000 -r 27c5c2979e32 execute_dwt_var_perClass.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/execute_dwt_var_perClass.xml	Thu Jan 23 12:31:07 2014 -0500
@@ -0,0 +1,105 @@
+<tool id="compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom" name="Compute P-values and Max Variances for Feature Occurrences" version="1.0.0">
+  <description>in one dataset using Discrete Wavelet Transfoms</description>
+  
+  <command interpreter="perl">
+  	execute_dwt_var_perClass.pl $inputFile $outputFile1 $outputFile2 $outputFile3
+  </command>
+  
+  <inputs>
+  	<param format="tabular" name="inputFile" type="data" label="Select the input file"/>	
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="outputFile1"/> 
+    <data format="tabular" name="outputFile2"/>
+    <data format="pdf" name="outputFile3"/>
+  </outputs>
+  	
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+This program generates plots and computes table matrix of maximum variances, p-values, and test orientations at multiple scales for the occurrences of a class of features in one dataset of DNA sequences using multiscale wavelet analysis technique. 
+
+The program assumes that the user has one set of DNA sequences, S, which consists of one or more sequences of equal length. Each sequence in S 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.
+
+The program has one input file obtained as follows:
+
+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 S, and builds a tabular file representing the count results in each interval of S. This is the input file of the program. 
+
+The program gives three output files:
+
+- The first output file is a TABULAR format file giving the scales at which each features has a maximum variances.
+- The second output file is a TABULAR format file representing the variances, p-values, and test orientation for the occurrences of features at each scale based on a random permutation test and using multiscale wavelet analysis technique.
+- The third output file is a PDF file plotting the wavelet variances of each feature at each scale.
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+- If the number of features is greater than 12, the program will divide each output file into subfiles, such that each subfile represents the results of a group of 12 features except the last subfile that will represents the results of the rest. For example, if the number of features is 17, the p-values file will consists of two subfiles, the first for the features 1-12 and the second for the features 13-17. As for the PDF file, it will consists of two pages in this case.
+- 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. 
+
+-----
+
+
+**Example**
+
+Counting the occurrences of 8 features (motifs) in 16 intervals (one line per interval) of set of DNA sequences in S gives the following tabular file::
+
+	deletionHoptspot	insertionHoptspot	dnaPolPauseFrameshift	indelHotspot	topoisomeraseCleavageSite	translinTarget		vDjRecombinationSignal		x-likeSite
+		226			403			416			221		1165			832				749			1056		
+		236			444			380			241		1223			746				782			1207	
+		242			496			391			195		1116			643				770			1219	
+		243			429			364			191		1118			694				783			1223	
+		244			410			371			236		1063			692				805			1233	
+		230			386			370			217		1087			657				787			1215	
+		275			404			402			214		1044			697				831			1188	
+		265			443			365			231		1086			694				782			1184	
+		255			390			354			246		1114			642				773			1176	
+		281			384			406			232		1102			719				787			1191	
+		263			459			369			251		1135			643				810			1215	
+		280			433			400			251		1159			701				777			1151	
+		278			385			382			231		1147			697				707			1161	
+		248			393			389			211		1162			723				759			1183	
+		251			403			385			246		1114			752				776			1153	
+		239			383			347			227		1172			759				789			1141	
+  
+We notice that the number of scales here is 4 because 16 = 2^4. Runnig the program on the above input file gives the following 3 output files:
+
+The first output file::
+
+	motifs			max_var	at scale
+	deletionHoptspot		NA
+	insertionHoptspot		NA
+	dnaPolPauseFrameshift		NA
+	indelHotspot			NA
+	topoisomeraseCleavageSite	3
+	translinTarget			NA
+	vDjRecombinationSignal		NA
+	x.likeSite			NA
+	
+The second output file::
+
+	motif				1_var		1_pval		1_test		2_var		2_pval		2_test		3_var		3_pval		3_test		4_var		4_pval		4_test
+	
+	deletionHoptspot		0.457		0.048		L		1.18		0.334		R		1.61		0.194		R		3.41		0.055		R
+	insertionHoptspot		0.556		0.109		L		1.34		0.272		R		1.59		0.223		R		2.02		0.157		R
+	dnaPolPauseFrameshift		1.42		0.089		R		0.66		0.331		L		0.421		0.305		L		0.121		0.268		L
+	indelHotspot			0.373		0.021		L		1.36		0.254		R		1.24		0.301		R		4.09		0.047		R
+	topoisomeraseCleavageSite	0.305		0.002		L		0.936		0.489		R		3.78		0.01		R		1.25		0.272		R
+	translinTarget			0.525		0.061		L		1.69		0.11		R		2.02		0.131		R		0.00891		0.069		L
+	vDjRecombinationSignal		0.68		0.138		L		0.957		0.46		R		2.35		0.071		R		1.03		0.357		R
+	x.likeSite			0.928		0.402		L		1.33		0.261		R		0.735		0.431		L		0.783		0.422		R
+
+The third output file:
+
+.. image:: ${static_path}/operation_icons/dwt_var_perClass.png
+
+  </help>  
+  
+</tool>