# HG changeset patch
# User iuc
# Date 1616147103 0
# Node ID 62adf13b86ea9fe1f96df828992d800675116949
# Parent  9fd8b69e6e683924a67ede56bf1bec0833e04d42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"

diff -r 9fd8b69e6e68 -r 62adf13b86ea dexseq.R
--- a/dexseq.R	Tue Feb 26 10:50:15 2019 -0500
+++ b/dexseq.R	Fri Mar 19 09:45:03 2021 +0000
@@ -1,12 +1,14 @@
 ## Setup R error handling to go to stderr
-options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+options(show.error.messages = F, error = function() {
+    cat(geterrmessage(), file = stderr()); q("no", 1, F)
+})
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 
 suppressPackageStartupMessages({
     library("DEXSeq")
-    library('getopt')
-    library('rjson')
+    library("getopt")
+    library("rjson")
 })
 
 
@@ -15,107 +17,107 @@
 
 #get options, using the spec as defined by the enclosed list.
 #we read the options from the default: commandArgs(TRUE).
-spec = matrix(c(
-    'verbose', 'v', 2, "integer",
-    'help', 'h', 0, "logical",
-    'gtf', 'a', 1, "character",
-    'outfile', 'o', 1, "character",
-    'reportdir', 'r', 1, "character",
-    'rds', 'd', 1, "character",
-    'factors', 'f', 1, "character",
-    'threads', 'p', 1, "integer",
-    'fdr', 'c', 1, "double"
-), byrow=TRUE, ncol=4);
-opt = getopt(spec);
+spec <- matrix(c(
+    "verbose", "v", 2, "integer",
+    "help", "h", 0, "logical",
+    "gtf", "a", 1, "character",
+    "outfile", "o", 1, "character",
+    "reportdir", "r", 1, "character",
+    "rds", "d", 1, "character",
+    "factors", "f", 1, "character",
+    "threads", "p", 1, "integer",
+    "fdr", "c", 1, "double"
+), byrow = TRUE, ncol = 4);
+opt <- getopt(spec);
 
 # if help was asked for print a friendly message
 # and exit with a non-zero error code
-if ( !is.null(opt$help) ) {
-    cat(getopt(spec, usage=TRUE));
-    q(status=1);
+if (!is.null(opt$help)) {
+    cat(getopt(spec, usage = TRUE));
+    q(status = 1);
 }
 
-trim <- function (x) gsub("^\\s+|\\s+$", "", x)
+trim <- function(x) gsub("^\\s+|\\s+$", "", x)
 opt$samples <- trim(opt$samples)
 opt$factors <- trim(opt$factors)
 
 parser <- newJSONParser()
-parser$addData( opt$factors )
-factorsList <- parser$getObject()
+parser$addData(opt$factors)
+factors_list <- parser$getObject()
 
-sampleTable<-data.frame()
-countFiles<-c()
-factorNames<-c()
-primaryFactor<-""
-for(factor in factorsList){
-    factorName<-factor[[1]]
-    factorNames<-append(factorNames, paste(factorName,"exon",sep=":"))
-    factorValuesMapList<-factor[[2]]
-    c = length(factorValuesMapList)
-    for (factorValuesMap in factorValuesMapList){
-        for(files in factorValuesMap){
-            for(file in files){
-                if(primaryFactor == "") {
-                    countFiles<-append(countFiles,file)
+sample_table <- data.frame()
+count_files <- c()
+factor_names <- c()
+primary_factor <- ""
+for (factor in factors_list) {
+    factor_name <- factor[[1]]
+    factor_names <- append(factor_names, paste(factor_name, "exon", sep = ":"))
+    factor_values_map_list <- factor[[2]]
+    c <- length(factor_values_map_list)
+    for (factorValuesMap in factor_values_map_list) {
+        for (files in factorValuesMap) {
+            for (file in files) {
+                if (primary_factor == "") {
+                    count_files <- append(count_files, file)
                 }
-                sampleTable[basename(file),factorName]<-paste(c,names(factorValuesMap),sep="_")
+                sample_table[basename(file), factor_name] <- paste(c, names(factorValuesMap), sep = "_")
             }
         }
-        c = c-1
+        c <- c - 1
     }
-    if(primaryFactor == ""){
-        primaryFactor <- factorName
+    if (primary_factor == "") {
+        primary_factor <- factor_name
     }
 }
 
-factorNames<-append(factorNames,"exon")
-factorNames<-append(factorNames,"sample")
-factorNames<-rev(factorNames)
-formulaFullModel <- as.formula(paste("", paste(factorNames, collapse=" + "), sep=" ~ "))
-factorNames <- head(factorNames,-1)
-formulaReducedModel <- as.formula(paste("", paste(factorNames, collapse=" + "), sep=" ~ "))
+factor_names <- append(factor_names, "exon")
+factor_names <- append(factor_names, "sample")
+factor_names <- rev(factor_names)
+formula_full_model <- as.formula(paste("", paste(factor_names, collapse = " + "), sep = " ~ "))
+factor_names <- head(factor_names, -1)
+formula_reduced_model <- as.formula(paste("", paste(factor_names, collapse = " + "), sep = " ~ "))
 
-sampleTable
-formulaFullModel
-formulaReducedModel
-primaryFactor
-countFiles
+sample_table
+formula_full_model
+formula_reduced_model
+primary_factor
+count_files
 opt$reportdir
 opt$threads
 getwd()
 
-dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= formulaFullModel, flattenedfile=opt$gtf)
+dxd <- DEXSeqDataSetFromHTSeq(count_files, sampleData = sample_table, design = formula_full_model, flattenedfile = opt$gtf)
 
 colData(dxd)
 dxd <- estimateSizeFactors(dxd)
 print("Estimated size factors")
 sizeFactors(dxd)
-BPPARAM=MulticoreParam(workers=opt$threads)
-dxd <- estimateDispersions(dxd, formula=formulaFullModel, BPPARAM=BPPARAM)
+bpparam <- MulticoreParam(workers = opt$threads)
+dxd <- estimateDispersions(dxd, formula = formula_full_model, BPPARAM = bpparam)
 print("Estimated dispersions")
-dxd <- testForDEU(dxd, reducedModel=formulaReducedModel, fullModel=formulaFullModel, BPPARAM=BPPARAM)
+dxd <- testForDEU(dxd, reducedModel = formula_reduced_model, fullModel = formula_full_model, BPPARAM = bpparam)
 print("tested for DEU")
-dxd <- estimateExonFoldChanges(dxd, fitExpToVar=primaryFactor, BPPARAM=BPPARAM)
+dxd <- estimateExonFoldChanges(dxd, fitExpToVar = primary_factor, BPPARAM = bpparam)
 print("Estimated fold changes")
 res <- DEXSeqResults(dxd)
 print("Results")
 table(res$padj <= opt$fdr)
-resSorted <- res[order(res$padj),]
-head(resSorted)
+res_sorted <- res[order(res$padj), ]
+head(res_sorted)
 
-export_table <- as.data.frame(resSorted)
+export_table <- as.data.frame(res_sorted)
 last_column <- ncol(export_table)
-for(i in 1:nrow(export_table)) {
-  export_table[i,last_column] <- paste(export_table[i,last_column][[1]],collapse=", ")
+for (i in seq_len(nrow(export_table))) {
+  export_table[i, last_column] <- paste(export_table[i, last_column][[1]], collapse = ", ")
 }
-write.table(export_table, file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE)
+write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, col.names = FALSE)
 print("Written Results")
 
-if ( !is.null(opt$rds) ) {
-    saveRDS(res, file="DEXSeqResults.rds")
+if (!is.null(opt$rds)) {
+    saveRDS(res, file = "DEXSeqResults.rds")
 }
 
-if ( !is.null(opt$reportdir) ) {
-    DEXSeqHTML(res, fitExpToVar=primaryFactor, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA"))
+if (!is.null(opt$reportdir)) {
+    DEXSeqHTML(res, fitExpToVar = primary_factor, path = opt$reportdir, FDR = opt$fdr, color = c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7", "#CEAEFF", "#EDC3C5", "#AAA8AA"))
 }
 sessionInfo()
diff -r 9fd8b69e6e68 -r 62adf13b86ea dexseq_helper.py
--- a/dexseq_helper.py	Tue Feb 26 10:50:15 2019 -0500
+++ b/dexseq_helper.py	Fri Mar 19 09:45:03 2021 +0000
@@ -1,4 +1,4 @@
-def validate_input( trans, error_map, param_values, page_param_map ):
+def validate_input(trans, error_map, param_values, page_param_map):
     """
         Validates the user input, before execution.
     """
@@ -13,7 +13,7 @@
         if fn in factor_name_list:
             factor_duplication = True
             break
-        factor_name_list.append( fn )
+        factor_name_list.append(fn)
 
         level_name_list = list()
 
@@ -22,15 +22,15 @@
             fl = factor[level]
             if fl in level_name_list:
                 level_duplication = True
-            level_name_list.append( fl )
+            level_name_list.append(fl)
 
         if level_duplication:
-            error_map['rep_factorName'] = [ dict() for t in factors ]
-            for i in range( len( factors ) ):
-                error_map['rep_factorName'][i]['FactorLevel1'] = [ {'factorLevel': 'Factor levels for each factor need to be unique'} for t in [factor['factorLevel1'], factor['factorLevel2']] ]
+            error_map['rep_factorName'] = [dict() for t in factors]
+            for i in range(len(factors)):
+                error_map['rep_factorName'][i]['FactorLevel1'] = [{'factorLevel': 'Factor levels for each factor need to be unique'} for t in [factor['factorLevel1'], factor['factorLevel2']]]
             break
 
     if factor_duplication:
-        error_map['rep_factorName'] = [ dict() for t in factors ]
-        for i in range( len( factors ) ):
+        error_map['rep_factorName'] = [dict() for t in factors]
+        for i in range(len(factors)):
             error_map['rep_factorName'][i]['factorName'] = 'Factor names need to be unique.'
diff -r 9fd8b69e6e68 -r 62adf13b86ea plotdexseq.R
--- a/plotdexseq.R	Tue Feb 26 10:50:15 2019 -0500
+++ b/plotdexseq.R	Fri Mar 19 09:45:03 2021 +0000
@@ -1,11 +1,13 @@
 ## Setup R error handling to go to stderr
-options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+options(show.error.messages = F, error = function() {
+    cat(geterrmessage(), file = stderr()); q("no", 1, F)
+})
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 
 suppressPackageStartupMessages({
     library("DEXSeq")
-    library('getopt')
+    library("getopt")
 })
 
 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
@@ -13,35 +15,35 @@
 
 #get options, using the spec as defined by the enclosed list.
 #we read the options from the default: commandArgs(TRUE).
-spec = matrix(c(
-    'rdata', 'r', 1, "character",
-    'primaryfactor', 'p', 1, "character",
-    'geneid', 'g', 1, "character",
-    'genefile', 'f', 1, "character",
-    'fdr', 'c', 1, "double",
-    'transcripts', 't', 1, "logical",
-    'names', 'a', 1, "logical",
-    'normcounts', 'n', 1, "logical",
-    'splicing', 's', 1, "logical"
-), byrow=TRUE, ncol=4);
-opt = getopt(spec);
+spec <- matrix(c(
+    "rdata", "r", 1, "character",
+    "primaryfactor", "p", 1, "character",
+    "geneid", "g", 1, "character",
+    "genefile", "f", 1, "character",
+    "fdr", "c", 1, "double",
+    "transcripts", "t", 1, "logical",
+    "names", "a", 1, "logical",
+    "normcounts", "n", 1, "logical",
+    "splicing", "s", 1, "logical"
+), byrow = TRUE, ncol = 4);
+opt <- getopt(spec);
 
 res <- readRDS(opt$rdata)
 
 if (!is.null(opt$genefile)) {
-	genes <- read.delim(opt$genefile, header=FALSE)
-	genes <- genes[, 1]
+    genes <- read.delim(opt$genefile, header = FALSE)
+    genes <- genes[, 1]
 } else {
-	genes <- opt$geneid
+    genes <- opt$geneid
 }
 
 pdf("plot.pdf")
-for (i in genes){
-	plotDEXSeq(res, i, FDR=opt$fdr, fitExpToVar=opt$primaryfactor,
-	    norCounts=opt$normcounts, expression=TRUE, splicing=opt$splicing,
-	    displayTranscripts=opt$transcripts, names=opt$names, legend=TRUE,
-	    color=NULL, color.samples=NULL, transcriptDb=NULL)
+for (i in genes) {
+    plotDEXSeq(res, i, FDR = opt$fdr, fitExpToVar = opt$primaryfactor,
+        norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing,
+        displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE,
+        color = NULL, color.samples = NULL, transcriptDb = NULL)
 }
 dev.off()
 
-sessionInfo()
\ No newline at end of file
+sessionInfo()