diff execute_dwt_var_perFeature.pl @ 3:6c29c7e347e8 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"

--- a/execute_dwt_var_perFeature.pl	Tue Aug 14 10:32:11 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,199 +0,0 @@
-#!/usr/bin/perl -w
-# Author: Erika Kvikstad
-
-use warnings;
-use IO::Handle;
-use POSIX qw(floor ceil);
-
-$usage = "execute_dwt_var_perFeature.pl [TABULAR.in] [FEATURE] [ALPHA] [TABULAR.out] [PDF.out] \n";
-die $usage unless @ARGV == 5;
-
-#get the input arguments
-my $inputFile = $ARGV[0];
-my @features = split(/,/,$ARGV[1]);
-my $features_count = scalar(@features);
-my $alpha = $ARGV[2];
-my $outFile1 = $ARGV[3];
-my $outFile2 = $ARGV[4];
-
-open (INPUT, "<", $inputFile) || die("Could not open file $inputFile \n");
-open (OUTPUT2, ">", $outFile1) || die("Could not open file $outFile1 \n");
-open (OUTPUT3, ">", $outFile2) || die("Could not open file $outFile2 \n");
-#open (ERROR,  ">", "error.txt")  or die ("Could not open file error.txt \n");
-
-# choosing meaningful names for the output files
-$pvalue = $outFile1; 
-$pdf = $outFile2; 
-
-# write R script
-$r_script = "get_dwt_varPermut.r"; 
-
-open(Rcmd, ">", "$r_script") or die "Cannot open $r_script \n\n";
-
-print Rcmd "
-	######################################################################
-	# plot multiscale wavelet variance 
-	# create null bands by permuting the original data series
-	# generate plots and table of wavelet variance including p-values
-	######################################################################
-	options(echo = FALSE)
-	#library(\"Rwave\");
-	#library(\"wavethresh\");
-	#library(\"waveslim\");
-	# turn off diagnostics for de-bugging only, turn back on for functional tests on test
-	suppressMessages(require(\"Rwave\",quietly=TRUE,warn.conflicts = FALSE));
-	suppressMessages(require(\"wavethresh\",quietly=TRUE,warn.conflicts = FALSE));
-	suppressMessages(require(\"waveslim\",quietly=TRUE,warn.conflicts = FALSE));
-	suppressMessages(require(\"bitops\",quietly=TRUE,warn.conflicts = FALSE));
-
-	# to determine if data is properly formatted 2^N observations
-	is.power2<- function(x){x && !(bitAnd(x,x - 1));}
-
-	# dwt : discrete wavelet transform using Haar wavelet filter, simplest wavelet function but later can modify to let user-define the wavelet filter function
-	dwt_var_permut_getMax <- function(data, names, alpha, filter = 1,family=\"DaubExPhase\", bc = \"symmetric\", method = \"kendall\", wf = \"haar\", boundary = \"reflection\") {
-		max_var = NULL;
-    		matrix = NULL;
-		title = NULL;
-    		final_pvalue = NULL;
-		J = NULL;
-		scale = NULL;
-		out = NULL;
-	
-	print(class(data));	
-    	print(names);
-	print(alpha);
-    	
-	par(mar=c(5,4,4,3),oma = c(4, 4, 3, 2), xaxt = \"s\", cex = 1, las = 1);
-   
-	title<-c(\"Wavelet\",\"Variance\",\"Pvalue\",\"Test\");
-	print(title);
-
-    	for(i in 1:length(names)){
-		temp = NULL;
-		results = NULL;
-		wave1.dwt = NULL;
-	
-		# if data fails formatting check, do something
-				
-		print(is.numeric(as.matrix(data)[, i]));
-		if(!is.numeric(as.matrix(data)[, i]))
-			stop(\"data must be a numeric vector\");
-		
-		print(length(as.matrix(data)[, i]));
-		print(is.power2(length(as.matrix(data)[, i])));
-		if(!is.power2(length(as.matrix(data)[, i])))	
-			stop(\"data length must be a power of two\");
-
-
-    		J <- wd(as.matrix(data)[, i], filter.number = filter, family=family, bc = bc)\$nlevels;
-		print(J);
-            	temp <- vector(length = J);
-               	wave1.dwt <- dwt(as.matrix(data)[, i], wf = wf, J, boundary = boundary); 
-		#print(wave1.dwt);
-                		
-                temp <- wave.variance(wave1.dwt)[-(J+1), 1];
-		print(temp);
-
-                #permutations code :
-                feature1 = NULL;
-		null = NULL;
-		var_lower=limit_lower=NULL;
-		var_upper=limit_upper=NULL;
-		med = NULL;
-
-		limit_lower = alpha/2*1000;
-		print(limit_lower);
-		limit_upper = (1-alpha/2)*1000;
-		print(limit_upper);
-		
-		feature1 = as.matrix(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,family=family ,bc = bc)\$nlevels;
-                       	var <- vector(length = length(null.levels));
-                       	null_wave1 <- dwt(nk_1, wf = wf, J, boundary = boundary);
-                       	var<- wave.variance(null_wave1)[-(null.levels+1), 1];
-                       	null= rbind(null, var);
-               }
-               null <- apply(null, 2, sort, na.last = TRUE);
-               var_lower <- null[limit_lower, ];
-               var_upper <- null[limit_upper, ];
-               med <- (apply(null, 2, median, na.rm = TRUE));
-
-               # plot
-               results <- cbind(temp, var_lower, var_upper);
-		print(results);
-                matplot(results, type = \"b\", pch = \"*\", lty = 1, col = c(1, 2, 2),xaxt='n',xlab=\"Wavelet Scale\",ylab=\"Wavelet variance\" );
-		mtext(names[i], side = 3, line = 0.5, cex = 1);
-		axis(1, at = 1:J , labels=c(2^(0:(J-1))), las = 3, cex.axis = 1);
-
-                # 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 =scale = NULL;
-			scale=2^(m-1);
-			#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])));
-                        	}
-			}
-			print(pv);
-			out<-rbind(out,c(paste(\"Scale\", scale, sep=\"_\"),format(temp[m], digits = 3),pv,tail));
-                }
-		final_pvalue <-rbind(final_pvalue, out);
-  	}
-	colnames(final_pvalue) <- title;
-    	return(final_pvalue);
-}\n";
-
-print Rcmd "
-# execute
-# read in data 
-data_test = final = NULL;
-sub = sub_names = NULL;
-data_test <- read.delim(\"$inputFile\",header=FALSE);
-pdf(file = \"$pdf\", width = 11, height = 8)\n";
-
-for ($x=0;$x<$features_count;$x++){	
-	$feature=$features[$x];
-print Rcmd "
-	if ($feature > ncol(data_test))
-		stop(\"column $feature doesn't exist\");	
-	sub<-data_test[,$feature];
-	#sub_names <- colnames(data_test);
-	sub_names<-colnames(data_test)[$feature];
-	final <- rbind(final,dwt_var_permut_getMax(sub, sub_names,$alpha));\n";
-}
-
-print Rcmd "
-
-	dev.off();
-	write.table(final, file = \"$pvalue\", sep = \"\\t\", quote = FALSE, row.names = FALSE);
-
-#eof\n";
-
-close Rcmd;
-system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
-
-#close the input and output and error files
-close(OUTPUT3);
-close(OUTPUT2);
-close(INPUT);