| Previous changeset 0:0b89b03ad760 (2014-01-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24" |
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modified:
execute_dwt_IvC_all.xml |
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added:
execute_dwt_IvC_all.R test-data/in1.tsv test-data/in2.tsv test-data/out2.pdf |
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removed:
execute_dwt_IvC_all.pl |
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| diff -r 0b89b03ad760 -r 506ae7b0d85d execute_dwt_IvC_all.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/execute_dwt_IvC_all.R Mon Jul 06 20:31:56 2020 -0400 |
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| @@ -0,0 +1,163 @@ +########################################################################################### +## code to do wavelet Indel vs. Control +## signal is the difference I-C; function is second moment i.e. variance from zero not mean +## to perform wavelet transf. of signal, scale-by-scale analysis of the function +## create null bands by permuting the original data series +## generate plots and table matrix of correlation coefficients including p-values +############################################################################################ +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_cor <- function(data_short, names_short, data_long, names_long, test, pdf, table, filter = 4, bc = "symmetric", wf = "haar", boundary = "reflection") { + print(test); + print(pdf); + print(table); + + pdf(file = pdf); + final_pvalue <- NULL; + title <- NULL; + + short_levels <- wavethresh::wd(data_short[, 1], filter.number = filter, bc = bc)$nlevels; + title <- c("motif"); + for (i in 1:short_levels) { + title <- c(title, paste(i, "moment2", sep = "_"), paste(i, "pval", sep = "_"), paste(i, "test", sep = "_")); + } + print(title); + + ## loop to compare a vs a + for (i in seq_len(length(names_short))) { + wave1_dwt <- NULL; + m2_dwt <- NULL; + diff <- NULL; + var_dwt <- NULL; + out <- NULL; + out <- vector(length = length(title)); + + print(names_short[i]); + print(names_long[i]); + + ## need exit if not comparing motif(a) vs motif(a) + if (names_short[i] != names_long[i]) { + stop(paste("motif", names_short[i], "is not the same as", names_long[i], sep = " ")); + } + else { + ## signal is the difference I-C data sets + diff <- data_short[, i] - data_long[, i]; + + ## normalize the signal + diff <- norm(diff); + + ## function is 2nd moment + ## 2nd moment m_j = 1/N[sum_N(W_j + V_J)^2] = 1/N sum_N(W_j)^2 + (X_bar)^2 + wave1_dwt <- waveslim::dwt(diff, wf = wf, short_levels, boundary = boundary); + var_dwt <- waveslim::wave.variance(wave1_dwt); + m2_dwt <- vector(length = short_levels) + for (level in 1:short_levels) { + m2_dwt[level] <- var_dwt[level, 1] + (mean(diff)^2); + } + + ## CI bands by permutation of time series + feature1 <- NULL; + feature2 <- NULL; + feature1 <- data_short[, i]; + feature2 <- data_long[, i]; + null <- NULL; + results <- NULL; + med <- NULL; + m2_25 <- NULL; + m2_975 <- NULL; + + for (k in 1:1000) { + nk_1 <- NULL; + nk_2 <- NULL; + m2_null <- NULL; + var_null <- NULL; + null_levels <- NULL; + null_wave1 <- NULL; + null_diff <- NULL; + nk_1 <- sample(feature1, length(feature1), replace = FALSE); + nk_2 <- sample(feature2, length(feature2), replace = FALSE); + null_levels <- wavethresh::wd(nk_1, filter.number = filter, bc = bc)$nlevels; + null_diff <- nk_1 - nk_2; + null_diff <- norm(null_diff); + null_wave1 <- waveslim::dwt(null_diff, wf = wf, short_levels, boundary = boundary); + var_null <- waveslim::wave.variance(null_wave1); + m2_null <- vector(length = null_levels); + for (level in 1:null_levels) { + m2_null[level] <- var_null[level, 1] + (mean(null_diff)^2); + } + null <- rbind(null, m2_null); + } + + null <- apply(null, 2, sort, na.last = TRUE); + m2_25 <- null[25, ]; + m2_975 <- null[975, ]; + med <- apply(null, 2, median, na.rm = TRUE); + + ## plot + results <- cbind(m2_dwt, m2_25, m2_975); + matplot(results, type = "b", pch = "*", lty = 1, col = c(1, 2, 2), xlab = "Wavelet Scale", ylab = c("Wavelet 2nd Moment", test), main = (names_short[i]), cex.main = 0.75); + abline(h = 1); + + ## get pvalues by comparison to null distribution + out <- c(names_short[i]); + for (m in seq_len(length(m2_dwt))) { + print(paste("scale", m, sep = " ")); + print(paste("m2", m2_dwt[m], sep = " ")); + print(paste("median", med[m], sep = " ")); + out <- c(out, format(m2_dwt[m], digits = 4)); + pv <- NULL; + if (is.na(m2_dwt[m])) { + pv <- "NA"; + } + else { + if (m2_dwt[m] >= med[m]) { + ## R tail test + tail <- "R"; + pv <- (length(which(null[, m] >= m2_dwt[m]))) / (length(na.exclude(null[, m]))); + } + else{ + if (m2_dwt[m] < med[m]) { + ## L tail test + tail <- "L"; + pv <- (length(which(null[, m] <= m2_dwt[m]))) / (length(na.exclude(null[, m]))); + } + } + } + out <- c(out, pv); + print(pv); + out <- c(out, tail); + } + final_pvalue <- rbind(final_pvalue, out); + print(out); + } + } + + colnames(final_pvalue) <- title; + write.table(final_pvalue, file = table, sep = "\t", quote = FALSE, row.names = FALSE); + dev.off(); +} +## execute +## read in data +args <- commandArgs(trailingOnly = TRUE) + +input_data <- read.delim(args[1]); +input_data_names <- colnames(input_data); + +control_data <- read.delim(args[2]); +control_data_names <- colnames(control_data); + +## call the test function to implement IvC test +dwt_cor(input_data, input_data_names, control_data, control_data_names, test = "IvC", pdf = args[3], table = args[4]); +print("done with the correlation test"); |
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| diff -r 0b89b03ad760 -r 506ae7b0d85d execute_dwt_IvC_all.pl --- a/execute_dwt_IvC_all.pl Mon Jan 27 09:25:56 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,210 +0,0 @@\n-#!/usr/bin/perl -w\n-use warnings;\n-use IO::Handle;\n-\n-$usage = "execute_dwt_IvC_all.pl [TABULAR.in] [TABULAR.in] [TABULAR.out] [PDF.out] \\n";\n-die $usage unless @ARGV == 4;\n-\n-#get the input arguments\n-my $firstInputFile = $ARGV[0];\n-my $secondInputFile = $ARGV[1];\n-my $firstOutputFile = $ARGV[2];\n-my $secondOutputFile = $ARGV[3];\n-\n-open (INPUT1, "<", $firstInputFile) || die("Could not open file $firstInputFile \\n");\n-open (INPUT2, "<", $secondInputFile) || die("Could not open file $secondInputFile \\n");\n-open (OUTPUT1, ">", $firstOutputFile) || die("Could not open file $firstOutputFile \\n");\n-open (OUTPUT2, ">", $secondOutputFile) || die("Could not open file $secondOutputFile \\n");\n-open (ERROR, ">", "error.txt") or die ("Could not open file error.txt \\n");\n-\n-#save all error messages into the error file $errorFile using the error file handle ERROR\n-STDERR -> fdopen( \\*ERROR, "w" ) or die ("Could not direct errors to the error file error.txt \\n");\n-\n-\n-print "There are two input data files: \\n";\n-print "The input data file is: $firstInputFile \\n";\n-print "The control data file is: $secondInputFile \\n";\n-\n-# IvC test\n-$test = "IvC";\n-\n-# construct an R script to implement the IvC test\n-print "\\n";\n-\n-$r_script = "get_dwt_IvC_test.r"; \n-print "$r_script \\n";\n-\n-# R script\n-open(Rcmd, ">", "$r_script") or die "Cannot open $r_script \\n\\n";\n-print Rcmd "\n- ###########################################################################################\n- # code to do wavelet Indel vs. Control\n- # signal is the difference I-C; function is second moment i.e. variance from zero not mean\n- # to perform wavelet transf. of signal, scale-by-scale analysis of the function \n- # create null bands by permuting the original data series\n- # generate plots and table matrix of correlation coefficients including p-values\n- ############################################################################################\n- library(\\"Rwave\\");\n- library(\\"wavethresh\\");\n- library(\\"waveslim\\");\n- \n- options(echo = FALSE)\n- \n- # normalize data\n- norm <- function(data){\n- v <- (data - mean(data))/sd(data);\n- if(sum(is.na(v)) >= 1){\n- v <- data;\n- }\n- return(v);\n- }\n- \n- dwt_cor <- function(data.short, names.short, data.long, names.long, test, pdf, table, filter = 4, bc = \\"symmetric\\", wf = \\"haar\\", boundary = \\"reflection\\") {\n- print(test);\n- print(pdf);\n- print(table);\n- \n- pdf(file = pdf);\n- final_pvalue = NULL;\n- title = NULL;\n- \n- short.levels <- wd(data.short[, 1], filter.number = filter, bc = bc)\\$nlevels;\n- title <- c(\\"motif\\");\n- for (i in 1:short.levels){\n- \ttitle <- c(title, paste(i, \\"moment2\\", sep = \\"_\\"), paste(i, \\"pval\\", sep = \\"_\\"), paste(i, \\"test\\", sep = \\"_\\"));\n- }\n- print(title);\n- \n- # loop to compare a vs a\n- for(i in 1:length(names.short)){\n- \t\twave1.dwt = NULL;\n- \t\tm2.dwt = diff = var.dwt = NULL;\n- \t\tout = NULL;\n- out <- vector(length = length(title));\n- \n- \t\tprint(names.short[i]);\n- \t\tprint(names.long[i]);\n- \n- \t\t# need exit if not comparing motif(a) vs motif(a)\n- \t\tif (names.short[i] != names.long[i]){\n- \tstop(paste(\\"motif\\", names.short[i], \\"is not the same as\\", names.long[i], sep = \\" \\"));\n- \t\t}\n- \t\telse {\n- \t# signal is the difference I-C data sets\n- diff<-data.short[,i]-data.long[,i];\n- \n- # normalize the signal\n- diff<-norm(diff);\n- \n- # function is 2nd moment\n- # 2nd moment m_j = 1/N[s'..b'LSE);\n- \t\tnk_2 <- sample(feature2, length(feature2), replace = FALSE);\n- \t\tnull.levels <- wd(nk_1, filter.number = filter, bc = bc)\\$nlevels;\n- \t\tnull_diff <- nk_1-nk_2;\n- \t\tnull_diff <- norm(null_diff);\n- \t\tnull_wave1 <- dwt(null_diff, wf = wf, short.levels, boundary = boundary);\n- var_null <- wave.variance(null_wave1);\n- \t\tm2_null <- vector(length = null.levels);\n- \t\tfor(level in 1:null.levels){\n- \tm2_null[level] <- var_null[level, 1] + (mean(null_diff)^2);\n- \t\t}\n- \t\tnull= rbind(null, m2_null);\n- \t\t}\n- \n- \t\tnull <- apply(null, 2, sort, na.last = TRUE);\n- \t\tm2_25 <- null[25,];\n- \t\tm2_975 <- null[975,];\n- \t\tmed <- apply(null, 2, median, na.rm = TRUE);\n-\n- \t\t# plot\n- \t\tresults <- cbind(m2.dwt, m2_25, m2_975);\n- \t\tmatplot(results, type = \\"b\\", pch = \\"*\\", lty = 1, col = c(1, 2, 2), xlab = \\"Wavelet Scale\\", ylab = c(\\"Wavelet 2nd Moment\\", test), main = (names.short[i]), cex.main = 0.75);\n- \t\tabline(h = 1);\n-\n- \t\t# get pvalues by comparison to null distribution\n- \t\tout <- c(names.short[i]);\n- \t\tfor (m in 1:length(m2.dwt)){\n- \tprint(paste(\\"scale\\", m, sep = \\" \\"));\n- print(paste(\\"m2\\", m2.dwt[m], sep = \\" \\"));\n- print(paste(\\"median\\", med[m], sep = \\" \\"));\n- out <- c(out, format(m2.dwt[m], digits = 4));\t\n- pv = NULL;\n- if(is.na(m2.dwt[m])){\n- \tpv <- \\"NA\\"; \n- } \n- else {\n- \tif (m2.dwt[m] >= med[m]){\n- \t# R tail test\n- tail <- \\"R\\";\n- pv <- (length(which(null[, m] >= m2.dwt[m])))/(length(na.exclude(null[, m])));\n- }\n- else{\n- if (m2.dwt[m] < med[m]){\n- \t# L tail test\n- tail <- \\"L\\";\n- pv <- (length(which(null[, m] <= m2.dwt[m])))/(length(na.exclude(null[, m])));\n- }\n- }\n- }\n- out <- c(out, pv);\n- print(pv); \n- out <- c(out, tail);\n- }\n- final_pvalue <-rbind(final_pvalue, out);\n- print(out);\n- }\n- }\n- \n- colnames(final_pvalue) <- title;\n- write.table(final_pvalue, file = table, sep = \\"\\\\t\\", quote = FALSE, row.names = FALSE);\n- dev.off();\n- }\\n";\n-\n-print Rcmd "\n- # execute\n- # read in data \n- \n- inputData <- read.delim(\\"$firstInputFile\\");\n- inputDataNames <- colnames(inputData);\n- \n- controlData <- read.delim(\\"$secondInputFile\\");\n- controlDataNames <- colnames(controlData);\n- \n- # call the test function to implement IvC test\n- dwt_cor(inputData, inputDataNames, controlData, controlDataNames, test = \\"$test\\", pdf = \\"$secondOutputFile\\", table = \\"$firstOutputFile\\");\n- print (\\"done with the correlation test\\");\n-\\n";\n-\n-print Rcmd "#eof\\n";\n-\n-close Rcmd;\n-\n-system("echo \\"wavelet IvC test started on \\`hostname\\` at \\`date\\`\\"\\n");\n-system("R --no-restore --no-save --no-readline < $r_script > $r_script.out\\n");\n-system("echo \\"wavelet IvC test ended on \\`hostname\\` at \\`date\\`\\"\\n");\n-\n-#close the input and output and error files\n-close(ERROR);\n-close(OUTPUT2);\n-close(OUTPUT1);\n-close(INPUT2);\n-close(INPUT1);\n\\ No newline at end of file\n' |
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| diff -r 0b89b03ad760 -r 506ae7b0d85d execute_dwt_IvC_all.xml --- a/execute_dwt_IvC_all.xml Mon Jan 27 09:25:56 2014 -0500 +++ b/execute_dwt_IvC_all.xml Mon Jul 06 20:31:56 2020 -0400 |
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| @@ -1,20 +1,35 @@ -<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"> +<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="1.0.1"> <description>between two datasets using Discrete Wavelet Transfoms</description> - - <command interpreter="perl"> - execute_dwt_IvC_all.pl $inputFile1 $inputFile2 $outputFile1 $outputFile2 + <requirements> + <requirement type="package" version="1.7.5">r-waveslim</requirement> + <requirement type="package" version="4.6.8">r-wavethresh</requirement> + </requirements> + <command detect_errors="exit_code"> + Rscript --vanilla '$__tool_directory__/execute_dwt_IvC_all.R' + '$inputFile1' + '$inputFile2' + '$outputFile2' + '$outputFile1' </command> - <inputs> - <param format="tabular" name="inputFile1" type="data" label="Select the first input file"/> - <param format="tabular" name="inputFile2" type="data" label="Select the second input file"/> + <param format="tabular" name="inputFile1" type="data" label="Select the first input file"/> + <param format="tabular" name="inputFile2" type="data" label="Select the second input file"/> </inputs> - <outputs> - <data format="tabular" name="outputFile1"/> - <data format="pdf" name="outputFile2"/> + <data format="tabular" name="outputFile1" label="${tool.name} on ${on_string}: statistics"/> + <data format="pdf" name="outputFile2" label="${tool.name} on ${on_string}: pdf"/> </outputs> - + <tests> + <test> + <param ftype="tabular" name="inputFile1" value="in1.tsv"/> + <param ftype="tabular" name="inputFile2" value="in2.tsv"/> + <output name="outputFile1" ftype="tabular"> + <assert_contents><has_line_matching expression="^motif\t1_moment2.*"/></assert_contents> + <assert_contents><has_line_matching expression="^translinTarget.*" /></assert_contents> + </output> + <output name="outputFile2" ftype="pdf" file="out2.pdf" compare="sim_size"/> + </test> + </tests> <help> .. class:: infomark |
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| diff -r 0b89b03ad760 -r 506ae7b0d85d test-data/in1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in1.tsv Mon Jul 06 20:31:56 2020 -0400 |
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| @@ -0,0 +1,17 @@ +deletionHoptspot insertionHoptspot dnaPolPauseFrameshift topoisomeraseCleavageSite translinTarget +269 366 330 238 1129 +239 328 327 283 1188 +254 351 358 297 1151 +262 371 355 256 1107 +254 361 352 234 1192 +265 354 367 240 1182 +255 359 333 235 1217 +271 389 387 272 1241 +240 305 341 249 1159 +272 351 337 257 1169 +275 351 337 233 1158 +305 331 361 253 1172 +277 341 343 253 1113 +266 362 355 267 1162 +235 326 329 241 1230 +254 335 360 251 1172 |
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| diff -r 0b89b03ad760 -r 506ae7b0d85d test-data/in2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in2.tsv Mon Jul 06 20:31:56 2020 -0400 |
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| @@ -0,0 +1,17 @@ +deletionHoptspot insertionHoptspot dnaPolPauseFrameshift topoisomeraseCleavageSite translinTarget +104 146 142 113 478 +89 146 151 94 495 +100 176 151 88 435 +96 163 128 114 468 +99 138 144 91 513 +112 126 162 106 468 +86 127 145 83 491 +104 145 171 110 496 +91 121 147 104 469 +103 141 145 98 458 +92 134 142 117 468 +97 146 145 107 471 +115 121 136 109 470 +113 135 138 101 491 +111 150 138 102 451 +94 128 151 138 481 |
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| diff -r 0b89b03ad760 -r 506ae7b0d85d test-data/out2.pdf |
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| Binary file test-data/out2.pdf has changed |