| Previous changeset 0:ba070efb6f78 (2018-07-03) |
|
Commit message:
planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty |
|
modified:
cat_2.pl |
|
added:
MClust.xml MClust_all.R MClust_all_test.R test-data/Clust.csv test-data/Clust.pdf test-data/EXP11_paraR_log.txt test-data/EXP11_paraR_log_properties_v1 |
| b |
| diff -r ba070efb6f78 -r f3fa21cda5f5 MClust.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MClust.xml Fri Aug 10 15:45:44 2018 -0400 |
| b |
| @@ -0,0 +1,43 @@ +<tool id="MClust" name="M-Clust" version="0.1.0"> + <description>Get Cluster of proteins</description> + <command interpreter="Rscript">MClust_all.R -f $input1 -c $input2 -s $Space_String -i $id_column -e $first_experiment -v $outputCSV -d $outputPDF</command> + <inputs> + <param format="data" name="input1" type="data" label="Proteins file"/> + <param format="data" name="input2" type="data" label="Control File"/> + <param type="integer" name="id_column" label="Column number of Prptein Id" value="1" min="1" /> + <param type="integer" name="first_experiment" label="Column number where the experiments start" value="0" min="0" /> + <param type="text" name="Space_String" label="Space String" value="." /> + </inputs> + <outputs> + <data format="pdf" name="outputPDF" /> + <data format="tabular" name="outputCSV" /> + </outputs> + + <tests> + <test> + <param name="input1" value="EXP11_paraR_log.txt"/> + <param name="input2" value="EXP11_paraR_log_properties_v1"/> + <param name="id_column" value="31"/> + <param name="first_experiment" value="0"/> + <param name="Space_String" value="."/> + <output name="outputCSV" file="Clust.csv"/> + <output name="outputPDF" file="Clust.pdf"/> + </test> + </tests> + + <help> +This tool executes a clustering, after a evaluation with ANOVA, works with data with at least three repetitions. + </help> + + <citations> + <citation type="bibtex"> + @misc{Concatenate, + author = {Application, Labis}, + year = 2018, + title = M-Clust, + publisher = labisapplications + } + </citation> + </citations> +</tool> + |
| b |
| diff -r ba070efb6f78 -r f3fa21cda5f5 MClust_all.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MClust_all.R Fri Aug 10 15:45:44 2018 -0400 |
| [ |
| b'@@ -0,0 +1,534 @@\n+###\r\n+# title: ""\r\n+# author: "Diego M. Riano-Pachon, Rodrigo R. Dorado Goitia"\r\n+# date: ""\r\n+# output: pdf\r\n+###\r\n+\r\n+###\r\n+# Description\r\n+###\r\n+\r\n+### Installers ###\r\n+# install.packages("qvalue")\r\n+# install.packages("ggplot2")\r\n+# install.packages("mclust")\r\n+# install.packages("reshape2")\r\n+# install.packages(\'getopt\')\r\n+\r\n+rm(list=ls())\r\n+\r\n+#Load required packages\r\n+suppressMessages(library(qvalue))\r\n+suppressMessages(library(ggplot2))\r\n+suppressMessages(library(mclust))\r\n+suppressMessages(library(reshape2))\r\n+suppressMessages(library(getopt))\r\n+\r\n+###\r\n+\r\n+# Set Functions\r\n+\r\n+# Set The directory to start the execution and read a csv file\r\n+# directoryName String Name of the directory.\r\n+# filename String Name of the csv file.\r\n+# Rodrigo Dorado\r\n+readCsvDirectory<-function(directoryName, filename, SpaceString) {\r\n+ setwd(directoryName)\r\n+ fileData <- read.csv(filename,\r\n+ sep = "\\t", \r\n+ header=TRUE, \r\n+ na.strings = \'NaN\',\r\n+ dec=SpaceString,\r\n+ stringsAsFactors=FALSE)\r\n+ return(fileData)\r\n+}\r\n+\r\n+# Print the dim, columns name and the first 5 rows of a variable\r\n+# dataToInform Object Name of the varaible.\r\n+# Rodrigo Dorado\r\n+printInfo <- function(dataToInform) {\r\n+ print(\'Length\')\r\n+ print(length(dataToInform))\r\n+ print(\'---------------\')\r\n+ print(\'Dim\')\r\n+ print(dim(dataToInform))\r\n+ print(\'***************\')\r\n+ print(\'Column Names\')\r\n+ print(colnames(dataToInform))\r\n+ print(\'_______________\')\r\n+ print(\'Firsts rows\')\r\n+ print(head(dataToInform))\r\n+ print(\'_______________\')\r\n+}\r\n+\r\n+## Put the id of protein as row name, get only the data of the experiments\r\n+## proteins matrix All the proteins data\r\n+## column_id int The number of the column where the is the id\r\n+## init_column int The number of the colmun of the initial experiment\r\n+## number_exp int The number of experiments\r\n+## Rodrigo Dorado \r\n+getDataofInfo <- function(proteins, column_id, init_column, number_exp) {\r\n+ selected_columns <- proteins[1:nrow(proteins), c(init_column:number_exp)]\r\n+ id_proteins_column <- proteins[1:nrow(proteins), column_id]\r\n+ ids <- matrix(, ncol = 1, nrow = nrow(proteins))\r\n+ j <- 1\r\n+ for(i in id_proteins_column){\r\n+ id_proteins_aux <- strsplit(i, ";")\r\n+ unlist(id_proteins_aux)\r\n+ ids[j] <- id_proteins_aux[[1]][1]\r\n+ j <- j + 1\r\n+ }\r\n+ row.names(selected_columns) <- ids\r\n+ return(selected_columns)\r\n+}\r\n+\r\n+## Verify if the protein contain at least one group with all the values different to NaN\r\n+## proteins matrix All the proteins data\r\n+## orderCondition int The division per experiment\r\n+## Rodrigo Dorado\r\n+VarifyAComplteGroup <- function(proteins, orderCondition) {\r\n+ protein_erase <- c()\r\n+ col_names <- colnames(proteins)\r\n+ ## Get every protein\r\n+ count <- 0\r\n+ for (protein in 1:nrow(proteins)) {\r\n+ ok_protein <- FALSE\r\n+ num_div <- ncol(orderCondition)\r\n+ columnNumber <- 1\r\n+ ## Move by a experiment\r\n+ for (result_exp in seq(1, nrow(orderCondition))) {\r\n+ ok_group <- TRUE\r\n+ pos_NaN <- c()\r\n+ pos_valid <- c()\r\n+ ## Get the name of the experiment\r\n+ column_name <- row.names(orderCondition)[result_exp]\r\n+ ## Move into the divisions\r\n+ for (div_pos in 1:num_div) {\r\n+ if (is.na(orderCondition[result_exp, div_pos])){\r\n+ break\r\n+ }\r\n+ pos <- columnNumber\r\n+ columnNumber <- columnNumber + 1\r\n+ ## pos <- result_exp + (div_pos - 1)\r\n+ ## check if is NaN\r\n+ if(is.na(proteins[protein, pos])){\r\n+ ok_group <- FALSE\r\n+ pos_NaN <- c(pos_NaN, pos)\r\n+ } else {\r\n+ pos_valid <- c(pos_valid, pos)\r\n+ }\r\n+ }\r\n+ ##Check if in the group, if the three are valid\r\n+ if (ok_group) {\r\n+ ok_protein <- TRUE\r\n+ }\r\n+ switch_var <- length(pos_NaN)\r\n+ allPos <- c(pos_valid, pos_NaN)\r\n+ ## Execute co'..b'aceString)\r\n+separateLine <- row.names(conditions[conditions[,1] == \'-- SEPARATE --\',])\r\n+columnsNameTime <- getNamesOfConditions(conditions, separateLine)\r\n+conditions <- conditions[1:(as.numeric(separateLine) - 1), ]\r\n+printInfo(conditions)\r\n+conditions[,1] <- gsub(" ", SpaceString, conditions[,1])\r\n+printInfo(conditions)\r\n+Column_division <- nrow(conditions)\r\n+orderCondition <- orderConditionData(conditions)\r\n+printInfo(orderCondition)\r\n+printInfo(All_proteins)\r\n+#createFolder(directory, project_name)\r\n+proteins_complete <- getDataofInfo(All_proteins, id_column, first_experiment, Column_division)\r\n+printInfo(proteins_complete)\r\n+proteins_New_column <- VarifyAComplteGroup(proteins_complete, orderCondition)\r\n+printInfo(proteins_New_column)\r\n+proteins_for_ANOVA <- proteins_New_column[,1:Column_division]\r\n+proteins <- proteins_New_column[,(Column_division + 1):ncol(proteins_New_column)]\r\n+printInfo(proteins_for_ANOVA)\r\n+printInfo(proteins)\r\n+#write.csv(proteins_for_ANOVA, "Proteins For Anova.csv",row.names = TRUE, quote = FALSE)\r\n+#write.csv(proteins, "Proteins With Conditions.csv",row.names = TRUE, quote = FALSE)\r\n+p_values <- calculateANOVA(proteins_for_ANOVA, orderCondition, ANOVA_type)\r\n+printInfo(p_values)\r\n+proteins <- mergeById(proteins, p_values)\r\n+printInfo(proteins)\r\n+selectedSignificantExpr <- selectSignificanProteinsExpression(proteins)\r\n+printInfo(selectedSignificantExpr)\r\n+Sig_Pro_Exp_ZValues <- getZValueSgnificantProteinExpression(selectedSignificantExpr)\r\n+printInfo(Sig_Pro_Exp_ZValues)\r\n+\r\n+clusters <- executeMClust(Sig_Pro_Exp_ZValues, directoryCSV$directory, directoryCSV$file)#\'clusters.csv\'\r\n+printInfo(clusters)\r\n+Sig_Pro_Exp_ZValues_melt <- getZvaluesMelt(Sig_Pro_Exp_ZValues, clusters, orderCondition, columnsNameTime)\r\n+\r\n+rects <- setBackGroundColors()\r\n+\r\n+##plot the result. note: make function(s)\r\n+plots_withBackground <- list()\r\n+plots_withOutBackground <- list()\r\n+for (clusterNumber in 1:max(clusters$Cluster)){\r\n+ averageProfile <- as.data.frame(matrix(ncol = nrow(orderCondition),nrow=1))\r\n+ timesCond <- row.names(orderCondition)\r\n+ colnames(averageProfile) <- timesCond\r\n+ for (cond in 1:nrow(orderCondition)) {\r\n+ averageProfile[timesCond[cond]] <- mean(selectedSignificantExpr[row.names(selectedSignificantExpr) %in% clusters[which(clusters$Cluster == clusterNumber),"ProteinID"], timesCond[cond]])\r\n+ }\r\n+ \r\n+ zval_DEGenes_cluster <- as.data.frame(t(scale(t(averageProfile))))\r\n+ zval_DEGenes_cluster$ClusterNumber <- clusterNumber\r\n+ zval_DEGenes_cluster_melt <- melt(zval_DEGenes_cluster, id.vars="ClusterNumber")\r\n+ zval_DEGenes_cluster_melt$ClusterNumber <- NULL\r\n+ colnames(zval_DEGenes_cluster_melt) <- c("Time","RelativeExpression")\r\n+ zval_DEGenes_cluster_melt$ProteinID <- "Average"\r\n+ \r\n+ for(cond in 1:nrow(orderCondition)) {\r\n+ zval_DEGenes_cluster_melt$Time2[zval_DEGenes_cluster_melt$Time == timesCond[cond]] <- as.numeric(columnsNameTime[timesCond[cond], 2])\r\n+ }\r\n+ \r\n+ numberGenes = length(unique(clusters[which(clusters$Cluster == clusterNumber),"ProteinID"]))\r\n+ \r\n+ outFilePlot1 = paste("cluster1",clusterNumber,"graphWithoutBackground","pdf",sep=".")\r\n+ outFilePlot2 = paste("cluster1",clusterNumber,"graphWithBackground","pdf",sep=".")\r\n+ \r\n+ p <- ggplot(Sig_Pro_Exp_ZValues_melt[ which(Sig_Pro_Exp_ZValues_melt$Cluster == clusterNumber),], aes(x = Time2, y = RelativeExpression, group = ProteinID)) + \r\n+ geom_line(col = "lightgray") + \r\n+ geom_line(data = zval_DEGenes_cluster_melt, aes(x = Time2, y = RelativeExpression)) +\r\n+ theme_bw() +\r\n+ xlab("Time point") +\r\n+ ylab("Relative expression") +\r\n+ ggtitle(paste("Cluster 1", clusterNumber, sep = ".")) +\r\n+ annotate("text", x = 3, y = 1, label = paste(numberGenes,"proteins", sep = " "))\r\n+ ##ggsave(filename = outFilePlot1, plot = p)\r\n+ plots_withOutBackground[[clusterNumber]] <- p\r\n+}\r\n+setwd(directoryPDF$directory)\r\n+savePlotPDF(directoryPDF$file, plots_withOutBackground)\n\\ No newline at end of file\n' |
| b |
| diff -r ba070efb6f78 -r f3fa21cda5f5 MClust_all_test.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MClust_all_test.R Fri Aug 10 15:45:44 2018 -0400 |
| b |
| @@ -0,0 +1,1 @@ +suppressMessages(library(mclust)) \ No newline at end of file |
| b |
| diff -r ba070efb6f78 -r f3fa21cda5f5 cat_2.pl --- a/cat_2.pl Tue Jul 03 17:34:13 2018 -0400 +++ b/cat_2.pl Fri Aug 10 15:45:44 2018 -0400 |
| [ |
| @@ -8,8 +8,7 @@ open FILE2, "<", $ARGV[1] or die $!; my @file2 = <FILE2>; - -open SEL, '>', $ARGV[2] or die $!; +open SEL, ">", $ARGV[2] or die $!; foreach (@file1) { print SEL $_; } |
| b |
| diff -r ba070efb6f78 -r f3fa21cda5f5 test-data/Clust.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Clust.csv Fri Aug 10 15:45:44 2018 -0400 |
| b |
| b'@@ -0,0 +1,735 @@\n+GeneID,Cluster\r\n+Cre01.g000900.t1.2,1\r\n+Cre01.g001100.t1.2,2\r\n+Cre01.g001750.t1.2,3\r\n+Cre01.g002500.t1.2,3\r\n+Cre01.g003550.t1.1,5\r\n+Cre01.g004350.t1.2,6\r\n+Cre01.g004450.t1.2,21\r\n+Cre01.g004900.t1.2,32\r\n+Cre01.g004950.t1.1,9\r\n+Cre01.g005050.t1.1,10\r\n+Cre01.g006950.t2.1,32\r\n+Cre01.g007051.t1.2,2\r\n+Cre01.g007700.t1.1,2\r\n+Cre01.g009350.t1.2,19\r\n+Cre01.g010400.t1.2,1\r\n+Cre01.g010900.t1.2,4\r\n+Cre01.g013700.t2.1,4\r\n+Cre01.g014350.t1.2,2\r\n+Cre01.g015000.t1.2,10\r\n+Cre01.g015350.t1.1,13\r\n+Cre01.g016514.t1.1,13\r\n+Cre01.g019250.t1.2,2\r\n+Cre01.g021251.t1.1,10\r\n+Cre01.g021600.t1.2,15\r\n+Cre01.g022500.t1.2,16\r\n+Cre01.g023350.t1.1,2\r\n+Cre01.g025250.t1.1,8\r\n+Cre01.g026450.t1.2,17\r\n+Cre01.g026550.t1.1,5\r\n+Cre01.g026600.t1.2,18\r\n+Cre01.g026900.t2.1,16\r\n+Cre01.g027550.t1.1,7\r\n+Cre01.g027800.t1.2,6\r\n+Cre01.g027950.t1.2,19\r\n+Cre01.g029650.t1.1,20\r\n+Cre01.g029750.t1.1,2\r\n+Cre01.g032300.t1.2,21\r\n+Cre01.g033400.t1.2,8\r\n+Cre01.g034000.t1.2,16\r\n+Cre01.g034400.t1.1,22\r\n+Cre01.g035350.t1.2,16\r\n+Cre01.g037850.t1.1,24\r\n+Cre01.g038850.t1.1,23\r\n+Cre01.g039250.t2.1,21\r\n+Cre01.g039300.t1.2,21\r\n+Cre01.g040000.t1.2,21\r\n+Cre01.g042200.t1.1,17\r\n+Cre01.g042750.t1.2,10\r\n+Cre01.g044800.t1.2,25\r\n+Cre01.g047750.t1.2,24\r\n+Cre01.g049000.t1.2,18\r\n+Cre01.g049500.t1.2,32\r\n+Cre01.g050850.t2.1,5\r\n+Cre01.g050950.t1.2,13\r\n+Cre01.g051100.t1.2,32\r\n+Cre01.g051500.t1.2,22\r\n+Cre01.g052100.t1.2,21\r\n+Cre01.g053000.t1.2,25\r\n+Cre01.g055420.t1.1,25\r\n+Cre01.g061077.t1.1,26\r\n+Cre01.g062172.t1.1,15\r\n+Cre02.g075700.t1.2,21\r\n+Cre02.g076350.t1.2,25\r\n+Cre02.g077750.t1.2,32\r\n+Cre02.g078507.t1.2,18\r\n+Cre02.g079500.t1.1,14\r\n+Cre02.g079550.t1.2,19\r\n+Cre02.g080200.t1.2,21\r\n+Cre02.g080350.t1.1,27\r\n+Cre02.g080700.t1.2,8\r\n+Cre02.g081050.t1.2,4\r\n+Cre02.g081250.t1.2,2\r\n+Cre02.g082250.t1.1,8\r\n+Cre02.g082877.t1.1,28\r\n+Cre02.g083800.t2.1,19\r\n+Cre02.g083950.t1.1,21\r\n+Cre02.g084000.t1.2,21\r\n+Cre02.g085450.t1.2,21\r\n+Cre02.g085900.t1.2,22\r\n+Cre02.g087450.t1.2,8\r\n+Cre02.g088200.t1.2,2\r\n+Cre02.g088900.t1.2,13\r\n+Cre02.g090850.t1.1,12\r\n+Cre02.g091050.t1.2,21\r\n+Cre02.g091700.t1.2,19\r\n+Cre02.g093450.t1.2,30\r\n+Cre02.g093650.t1.2,10\r\n+Cre02.g095146.t1.1,2\r\n+Cre02.g096150.t1.2,16\r\n+Cre02.g097400.t1.2,21\r\n+Cre02.g097550.t1.2,22\r\n+Cre02.g098450.t1.2,24\r\n+Cre02.g099850.t1.1,4\r\n+Cre02.g101350.t1.2,21\r\n+Cre02.g101400.t1.2,10\r\n+Cre02.g106600.t1.2,3\r\n+Cre02.g108850.t1.2,24\r\n+Cre02.g113200.t1.1,10\r\n+Cre02.g114450.t1.2,8\r\n+Cre02.g114600.t1.2,25\r\n+Cre02.g115200.t1.2,21\r\n+Cre02.g116750.t2.1,25\r\n+Cre02.g118950.t1.2,4\r\n+Cre02.g120150.t1.2,10\r\n+Cre02.g141400.t1.2,18\r\n+Cre02.g143050.t1.2,24\r\n+Cre02.g143200.t1.1,11\r\n+Cre02.g143250.t1.2,32\r\n+Cre02.g143307.t1.1,8\r\n+Cre02.g143650.t2.1,23\r\n+Cre02.g143667.t1.1,19\r\n+Cre02.g145800.t1.2,8\r\n+Cre02.g146250.t1.2,5\r\n+Cre02.g147302.t1.1,5\r\n+Cre02.g147900.t4.1,24\r\n+Cre03.g144627.t1.1,4\r\n+Cre03.g145507.t1.1,16\r\n+Cre03.g145647.t1.1,8\r\n+Cre03.g145727.t1.1,18\r\n+Cre03.g145747.t1.1,29\r\n+Cre03.g145967.t1.1,3\r\n+Cre03.g146167.t1.1,29\r\n+Cre03.g146187.t1.1,10\r\n+Cre03.g146247.t1.1,32\r\n+Cre03.g146527.t1.1,2\r\n+Cre03.g149100.t1.2,6\r\n+Cre03.g149250.t1.2,2\r\n+Cre03.g152750.t1.1,12\r\n+Cre03.g156050.t1.2,21\r\n+Cre03.g156900.t1.2,22\r\n+Cre03.g157700.t1.2,25\r\n+Cre03.g158000.t1.2,13\r\n+Cre03.g158800.t3.1,8\r\n+Cre03.g158900.t1.2,13\r\n+Cre03.g160500.t1.2,29\r\n+Cre03.g164300.t1.2,11\r\n+Cre03.g171950.t1.1,16\r\n+Cre03.g172000.t1.2,4\r\n+Cre03.g172850.t1.2,12\r\n+Cre03.g175200.t1.2,8\r\n+Cre03.g175400.t2.1,31\r\n+Cre03.g176250.t1.2,10\r\n+Cre03.g178250.t1.2,11\r\n+Cre03.g179860.t1.1,6\r\n+Cre03.g180750.t1.2,4\r\n+Cre03.g181500.t1.2,8\r\n+Cre03.g184700.t1.2,10\r\n+Cre03.g185550.t1.2,21\r\n+Cre03.g187450.t1.2,4\r\n+Cre03.g189500.t1.2,19\r\n+Cre03.g189800.t1.2,25\r\n+Cre03.g189950.t1.2,12\r\n+Cre03.g190100.t1.1,21\r\n+Cre03.g192850.t1.2,20\r\n+Cre03.g193850.t1.2,32\r\n+Cre03.g194200.t1.2,4\r\n+Cre03.g194350.t1.2,20\r\n+Cre03.g194400.t1.2,21\r\n+Cre03.g194850.t1.2,32\r\n+Cre03.g195388.t1.1,3\r\n+Cre03.g195650.t1.2,11\r\n+Cre03.g198950.t1.2,25\r\n+Cre03.g199000.t1.2,19\r\n+Cre03.g199535.t1.1,29\r\n+Cre03.g199647.t1.1,1\r\n+Cre03.g199900.t1.2,3\r\n+Cre03.g200250.t1.2,13\r\n+Cre03.g20'..b'.2,1\r\n+Cre12.g538500.t1.1,9\r\n+Cre12.g539100.t1.1,32\r\n+Cre12.g540650.t1.2,37\r\n+Cre12.g542350.t1.2,9\r\n+Cre12.g546050.t1.2,9\r\n+Cre12.g548950.t1.2,8\r\n+Cre12.g549350.t1.2,4\r\n+Cre12.g549550.t1.2,19\r\n+Cre12.g551352.t1.1,31\r\n+Cre12.g552200.t1.2,32\r\n+Cre12.g554800.t1.2,21\r\n+Cre12.g554850.t1.2,32\r\n+Cre12.g556050.t1.2,4\r\n+Cre12.g556250.t1.2,8\r\n+Cre12.g556600.t1.2,3\r\n+Cre12.g557600.t1.1,18\r\n+Cre12.g559250.t1.2,10\r\n+Cre12.g560150.t1.2,32\r\n+Cre12.g560900.t1.2,28\r\n+Cre12.g560950.t1.2,2\r\n+Cre13.g565450.t1.2,2\r\n+Cre13.g565800.t1.2,19\r\n+Cre13.g566000.t1.2,13\r\n+Cre13.g566650.t2.1,32\r\n+Cre13.g567450.t1.2,32\r\n+Cre13.g567600.t1.2,32\r\n+Cre13.g567700.t1.2,10\r\n+Cre13.g567850.t1.2,27\r\n+Cre13.g567950.t1.2,5\r\n+Cre13.g568650.t1.2,21\r\n+Cre13.g568800.t1.2,19\r\n+Cre13.g573250.t1.2,32\r\n+Cre13.g573351.t1.2,22\r\n+Cre13.g577100.t1.2,24\r\n+Cre13.g577900.t1.2,20\r\n+Cre13.g579566.t2.1,22\r\n+Cre13.g580850.t2.1,24\r\n+Cre13.g581650.t1.2,4\r\n+Cre13.g582800.t1.2,25\r\n+Cre13.g583550.t1.2,32\r\n+Cre13.g587050.t1.2,12\r\n+Cre13.g591951.t1.1,25\r\n+Cre13.g592200.t1.2,25\r\n+Cre13.g603700.t1.2,10\r\n+Cre13.g603850.t1.2,12\r\n+Cre13.g603900.t1.2,5\r\n+Cre13.g604650.t2.1,4\r\n+Cre13.g605150.t1.2,1\r\n+Cre14.g608800.t1.2,5\r\n+Cre14.g612450.t1.2,13\r\n+Cre14.g612633.t1.1,25\r\n+Cre14.g612800.t1.2,8\r\n+Cre14.g614300.t1.2,32\r\n+Cre14.g614350.t1.2,37\r\n+Cre14.g614900.t2.1,2\r\n+Cre14.g616100.t1.1,6\r\n+Cre14.g616600.t1.2,2\r\n+Cre14.g617900.t1.2,21\r\n+Cre14.g619133.t1.1,10\r\n+Cre14.g619166.t1.1,8\r\n+Cre14.g621450.t1.2,21\r\n+Cre14.g621650.t1.1,4\r\n+Cre14.g625400.t1.1,2\r\n+Cre14.g626500.t1.2,3\r\n+Cre14.g627850.t1.2,16\r\n+Cre14.g630100.t1.2,4\r\n+Cre14.g630847.t1.1,4\r\n+Cre15.g635067.t1.1,26\r\n+Cre15.g635600.t1.2,3\r\n+Cre15.g635850.t2.1,32\r\n+Cre15.g636050.t1.2,6\r\n+Cre15.g636750.t1.2,34\r\n+Cre15.g636800.t1.1,17\r\n+Cre15.g638400.t1.2,34\r\n+Cre15.g638500.t1.2,10\r\n+Cre15.g641000.t2.1,2\r\n+Cre15.g641600.t1.2,3\r\n+Cre15.g643550.t1.2,11\r\n+Cre15.g643600.t1.2,3\r\n+Cre16.g649350.t1.1,5\r\n+Cre16.g650550.t2.1,4\r\n+Cre16.g650600.t1.2,19\r\n+Cre16.g652550.t1.2,13\r\n+Cre16.g654500.t1.1,24\r\n+Cre16.g655150.t1.2,28\r\n+Cre16.g656400.t1.2,21\r\n+Cre16.g659950.t1.1,13\r\n+Cre16.g660150.t1.2,7\r\n+Cre16.g661050.t1.2,21\r\n+Cre16.g661350.t1.2,3\r\n+Cre16.g663900.t1.2,21\r\n+Cre16.g664550.t1.2,13\r\n+Cre16.g665250.t1.2,2\r\n+Cre16.g666301.t1.2,3\r\n+Cre16.g668150.t1.2,5\r\n+Cre16.g669550.t1.2,28\r\n+Cre16.g672300.t1.2,2\r\n+Cre16.g672385.t1.1,38\r\n+Cre16.g672650.t1.2,25\r\n+Cre16.g676314.t1.1,3\r\n+Cre16.g677000.t1.2,19\r\n+Cre16.g677026.t1.1,12\r\n+Cre16.g677500.t1.2,19\r\n+Cre16.g680000.t1.2,10\r\n+Cre16.g680700.t1.2,4\r\n+Cre16.g682300.t1.2,3\r\n+Cre16.g682800.t1.2,32\r\n+Cre16.g684750.t1.2,5\r\n+Cre16.g685550.t1.2,3\r\n+Cre16.g687182.t1.1,19\r\n+Cre16.g687300.t1.2,11\r\n+Cre16.g689087.t1.1,15\r\n+Cre16.g689647.t1.1,8\r\n+Cre16.g690431.t2.1,12\r\n+Cre16.g691850.t1.2,25\r\n+Cre16.g692901.t1.1,11\r\n+Cre16.g694850.t1.2,25\r\n+Cre16.g695050.t1.2,36\r\n+Cre17.g698000.t1.2,25\r\n+Cre17.g698450.t1.2,4\r\n+Cre17.g699000.t2.1,23\r\n+Cre17.g700750.t1.2,12\r\n+Cre17.g701200.t2.1,3\r\n+Cre17.g701500.t1.2,8\r\n+Cre17.g701700.t2.1,7\r\n+Cre17.g702200.t1.2,34\r\n+Cre17.g702650.t1.1,33\r\n+Cre17.g703700.t1.1,10\r\n+Cre17.g703900.t1.2,32\r\n+Cre17.g705000.t1.2,2\r\n+Cre17.g706600.t1.2,7\r\n+Cre17.g708300.t1.2,5\r\n+Cre17.g708600.t1.2,10\r\n+Cre17.g708750.t1.2,35\r\n+Cre17.g714600.t1.2,10\r\n+Cre17.g714650.t1.2,10\r\n+Cre17.g715250.t1.2,4\r\n+Cre17.g715300.t1.2,31\r\n+Cre17.g715350.t2.1,11\r\n+Cre17.g715500.t1.2,22\r\n+Cre17.g721500.t1.2,25\r\n+Cre17.g721650.t1.2,21\r\n+Cre17.g721700.t1.2,18\r\n+Cre17.g723650.t1.2,3\r\n+Cre17.g724200.t1.2,35\r\n+Cre17.g724350.t1.2,8\r\n+Cre17.g724550.t1.2,10\r\n+Cre17.g727300.t1.2,10\r\n+Cre17.g727950.t1.1,6\r\n+Cre17.g729150.t1.2,6\r\n+Cre17.g734100.t1.2,2\r\n+Cre17.g734200.t1.2,4\r\n+Cre17.g734450.t1.2,21\r\n+Cre17.g734500.t1.2,10\r\n+Cre17.g734900.t2.1,2\r\n+Cre17.g737050.t1.2,10\r\n+Cre17.g738300.t1.2,21\r\n+Cre17.g741200.t1.2,2\r\n+Cre17.g741450.t1.2,21\r\n+Cre17.g741850.t1.2,25\r\n+Cre17.g742300.t1.1,12\r\n+Cre17.g746597.t2.1,18\r\n+Cre17.g746997.t1.1,25\r\n+Cre18.g749497.t1.1,2\r\n+Cre18.g750047.t1.1,19\r\n+Cre19.g750147.t1.1,8\r\n+Cre19.g750547.t4.1,10\r\n+Cre24.g755497.t1.1,20\r\n+Cre48.g761197.t1.1,21\r\n' |
| b |
| diff -r ba070efb6f78 -r f3fa21cda5f5 test-data/Clust.pdf |
| b |
| Binary file test-data/Clust.pdf has changed |
| b |
| diff -r ba070efb6f78 -r f3fa21cda5f5 test-data/EXP11_paraR_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EXP11_paraR_log.txt Fri Aug 10 15:45:44 2018 -0400 |
| b |
| b'@@ -0,0 +1,1395 @@\n+LFQ intensity 11_TP5_1\tLFQ intensity 11_TP5_2\tLFQ intensity 11_TP5_3\tLFQ intensity 11_TP6_1\tLFQ intensity 11_TP6_2\tLFQ intensity 11_TP6_3\tLFQ intensity 11_TP7_1\tLFQ intensity 11_TP7_2\tLFQ intensity 11_TP7_3\tLFQ intensity 11_TP9_1\tLFQ intensity 11_TP9_2\tLFQ intensity 11_TP9_3\tLFQ intensity 11_TP10_1\tLFQ intensity 11_TP10_2\tLFQ intensity 11_TP10_3\tLFQ intensity 11_TP11_1\tLFQ intensity 11_TP11_2\tLFQ intensity 11_TP11_3\tLFQ intensity 11_TP12_1\tLFQ intensity 11_TP12_2\tLFQ intensity 11_TP12_3\tLFQ intensity 11_TP14_1\tLFQ intensity 11_TP14_2\tLFQ intensity 11_TP14_3\tLFQ intensity 11_TP15_1\tLFQ intensity 11_TP15_2\tLFQ intensity 11_TP15_3\tLFQ intensity 11_TP16_1\tLFQ intensity 11_TP16_2\tLFQ intensity 11_TP16_3\tMajority protein IDs\r\n+20.03711\t19.68753\t19.66075\t19.5736\t19.86575\t19.64171\t19.80371\t19.68789\t19.64577\t19.5382\t19.72392\t19.54049\t19.68777\t19.58613\t19.45117\t19.7536\t19.69086\t19.72704\t19.61459\t19.75382\t19.71609\t19.89024\t19.66466\t19.80895\t19.89024\t19.82533\t19.7277\t20.28828\t19.62519\t19.81182\tCre01.g000350.t1.1\r\n+NaN\t16.57753\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\t16.53616\tNaN\tNaN\t16.56625\tNaN\t17.63453\t17.36547\t17.35552\t17.86048\t18.39301\t17.97668\t17.98549\t17.92561\t18.37088\tCre01.g000900.t1.2\r\n+18.79265\t18.68127\t18.78245\t18.76704\t18.82619\t18.94186\t18.89202\t19.13819\t18.90721\t18.87939\t19.02948\t18.79725\t18.75861\t18.91199\t18.95111\t19.03397\t19.26659\t18.93641\t19.19246\t19.11388\t19.10991\t19.18819\t19.26941\t19.29852\t18.95985\t19.34882\t19.15682\t19.06949\t19.02372\t19.03368\tCre01.g001100.t1.2\r\n+18.14634\t17.78277\t17.62728\t18.15709\t18.24961\t17.58864\t18.25912\t18.22374\t17.38364\t18.03939\t17.827\t18.66758\t17.87634\tNaN\tNaN\tNaN\tNaN\t18.51768\t17.91666\t17.55255\t17.47809\t17.84402\t17.85878\tNaN\t16.90654\tNaN\tNaN\tNaN\t17.20791\tNaN\tCre01.g001750.t1.2\r\n+20.66388\t20.48611\t20.39843\t20.62069\t20.82687\t20.35283\t20.81792\t20.71003\t20.66414\t20.80577\t20.86499\t20.49209\t20.69668\t20.55328\t20.61944\t20.88092\t20.85377\t21.00072\t20.9338\t20.91933\t20.90727\t21.03638\t20.61531\t20.7866\t20.67297\t20.50853\t20.73958\t20.97365\t20.82788\t20.62712\tCre01.g002300.t1.2\r\n+20.80239\t20.96268\t21.07045\t20.97183\t21.06494\t20.91042\t21.33887\t21.10079\t21.26075\t21.1695\t20.87222\t21.0794\t21.06789\t21.11006\t21.2408\t21.0256\t21.41473\t21.33685\t21.41787\t21.22099\t21.51229\t21.11273\t21.08453\t21.19087\t20.52258\t20.66709\t20.68902\t19.62991\t20.34386\t20.22223\tCre01.g002500.t1.2\r\n+16.34391\tNaN\tNaN\tNaN\tNaN\tNaN\t16.39087\t16.5454\t16.07192\t16.62171\tNaN\tNaN\tNaN\tNaN\tNaN\t15.71628\t16.18307\t16.33557\t15.99305\t16.35456\t16.04147\tNaN\t16.30775\tNaN\tNaN\t16.81616\t16.55229\tNaN\t16.98826\t17.15956\tCre01.g003550.t1.1\r\n+18.78315\t18.94997\t19.11946\t18.88405\t18.89412\t19.15192\t18.50533\t18.70124\t18.97586\t19.10544\t18.71756\t19.24621\t19.16967\t19.05081\t19.08223\t19.18988\t18.69571\t18.71304\t18.76714\t18.57622\t19.06268\t18.82808\t18.66508\t18.96652\t19.03593\t18.79839\t19.01258\t18.59073\t18.79265\t18.93672\tCre01.g004300.t1.2\r\n+NaN\tNaN\t15.96436\t16.0111\tNaN\tNaN\tNaN\tNaN\tNaN\t16.10148\tNaN\tNaN\t16.12455\t16.10793\tNaN\tNaN\t16.24226\tNaN\t16.12854\t16.15008\tNaN\t16.39918\tNaN\tNaN\t16.27383\t16.09315\t16.72227\t16.32316\tNaN\t16.30643\tCre01.g004350.t1.2\r\n+NaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\t16.76979\tNaN\tNaN\tNaN\tNaN\t17.1947\tNaN\tCre01.g004400.t1.2\r\n+17.7384\tNaN\tNaN\tNaN\t17.82513\tNaN\tNaN\t17.81697\tNaN\t18.07739\t17.66303\tNaN\t17.66886\tNaN\tNaN\t18.02388\tNaN\t17.56473\t16.56302\t17.53746\t17.65634\t17.15244\tNaN\t17.50246\t17.7546\t17.34785\t17.22619\t17.22308\t17.25248\t17.28437\tCre01.g004450.t1.2\r\n+19.07843\t18.86084\t18.90545\t19.09192\t19.1585\t18.79392\t19.2105\t18.87622\t18.93874\t18.8287\t19.00435\t18.8135\t18.87397\t18.71977\t18.80079\t19.19453\t19.02315\t18.8558\t19.06789\t19.11713\t19.0016\t19.44982\t19.08338\t18.96045\t18.95043\t19.13726\t18.96067\t19.13904\t19.2761\t18.7695\tCre01.g004500.t1.2\r\n+17.86006\tNaN\tNaN\t17.48298\t17.63976\tNaN\t17.82712\t17.80423\t17.71572\tNaN\t18.26756\t17.45764\t17.53587\tNaN\t17.67307\t17.71492\tNaN\t17.69934\tNaN\t17.67342\t17.8104\t18.53066\t18.34278\t18.21798\t17.9822\t18.145\t17.67232\t18.45764\t18.17942\t18.15165\tCre01.g004900.t1.2\r\n+NaN\t16.67'..b'18.68736\t18.44225\t18.81093\t18.87753\t18.76549\t19.03955\t19.00903\t18.99231\t18.90627\t19.31739\t19.02996\tCre17.g741850.t1.2\r\n+NaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\t16.78839\tNaN\tNaN\t16.74517\t16.79246\t16.74767\tNaN\tNaN\t16.87051\t16.59604\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\t16.50535\t16.80574\t16.59792\tNaN\t16.75968\tNaN\tNaN\tCre17.g742200.t1.1\r\n+17.31646\t17.60979\t17.32184\tNaN\tNaN\tNaN\tNaN\tNaN\t17.34516\t17.50393\tNaN\tNaN\t16.90419\tNaN\t17.44006\tNaN\t17.47864\tNaN\tNaN\t17.39079\t17.56078\tNaN\tNaN\tNaN\t17.66206\tNaN\t17.56078\tNaN\t17.56287\tNaN\tCre17.g742300.t1.1\r\n+17.65606\t18.33447\t17.60205\t18.09636\tNaN\tNaN\tNaN\tNaN\t18.04457\tNaN\t17.80751\t18.63329\tNaN\t17.92335\t17.77423\t18.08187\t17.47643\t18.29988\t17.8629\t17.30001\t17.49646\t17.9798\t17.70597\t17.81441\tNaN\t17.80051\t17.95384\t18.14584\t17.89735\t18.13546\tCre17.g743897.t1.1\r\n+17.90689\t18.33398\t18.02832\t18.11908\t18.22515\t18.02426\t17.76442\t17.6363\t17.33211\t17.81021\t17.69418\t17.51968\t17.53465\t17.99336\t17.50866\t17.60371\t17.67342\t17.16153\t17.53207\t17.58813\t17.49833\t16.96927\t17.23594\tNaN\t17.0578\t16.30642\tNaN\tNaN\tNaN\tNaN\tCre17.g746597.t2.1;Cre17.g746597.t1.1\r\n+18.71569\t18.03085\t18.28261\t18.35303\t18.22303\t17.80291\t18.40719\t18.58101\t18.86463\t17.85166\t18.84821\t18.07916\t18.65508\t18.69374\t18.463\t18.15531\t18.11573\t18.82087\t18.68575\t18.67259\t18.4679\t19.25868\t19.17009\t19.04059\t20.44415\t20.11972\t19.68548\t20.62221\t20.38585\t20.62916\tCre17.g746997.t1.1\r\n+18.69663\t18.51618\t18.91254\t19.21457\t18.83763\t18.99184\t18.84156\t18.73301\t19.16992\t19.10411\t18.87403\t18.76846\t18.5856\t19.23386\t18.97309\t18.82972\t18.47017\t19.15465\t18.63392\t18.95325\t19.05468\t19.39753\t19.24209\t18.92231\t19.01544\t19.20046\t19.07648\t19.17099\t18.59918\t18.78373\tCre18.g749447.t2.1;Cre18.g749447.t1.1\r\n+18.79424\t18.72504\t19.20789\t18.94455\t19.14138\t19.15108\t18.98826\t19.0764\t19.17358\t18.99139\t19.01544\t18.82087\t18.79475\t18.97883\t18.8839\t19.03432\t19.05494\t19.1747\t19.03786\t18.9734\t19.04847\t19.32915\t19.16683\t19.33884\t19.02624\t18.94966\t19.32369\t19.42403\t19.2791\t19.35653\tCre18.g749497.t1.1\r\n+18.6095\t19.09128\t18.79687\t18.70641\t19.17762\t18.76069\t18.79795\t18.55375\t18.65032\t18.73856\t18.86952\t18.4737\t18.83282\t18.81199\t18.5417\t18.76477\t18.57167\t18.55708\t18.42312\t18.74983\t18.65414\t19.03074\t19.07538\t18.86704\t19.0777\t18.87081\t19.0278\t18.43376\t18.99775\t18.92152\tCre18.g749847.t2.1;Cre18.g749847.t1.1\r\n+19.57937\t19.4433\t18.98921\t19.30338\t19.27102\t18.91415\t19.35664\t20.31363\t19.82588\t20.39215\t20.98954\t20.35456\t20.71733\t21.0442\t20.72775\t21.32954\t20.99666\t21.09745\t21.26482\t21.33789\t21.13865\t21.54548\t21.84877\t21.52272\t21.78995\t22.10255\t21.65189\t21.66579\t21.43135\t21.12143\tCre18.g750047.t1.1\r\n+NaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\t15.40205\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\t16.25411\t16.25857\t16.19399\t16.16761\tNaN\t16.91134\tNaN\tNaN\tNaN\tCre19.g750147.t1.1\r\n+19.25758\t19.29123\t19.40258\t19.2739\t19.10889\t19.37687\t19.09159\t19.10539\t19.35242\t19.15135\t19.48142\t19.25893\t19.25271\t19.39814\t19.03915\t19.22084\t19.39615\t19.47243\t19.28448\t19.41652\t19.58665\t19.33787\t19.72186\t19.74445\t19.97603\t20.26934\t20.05788\t20.03939\t20.02418\t20.09326\tCre19.g750547.t4.1;Cre19.g750547.t3.1;Cre19.g750547.t2.1;Cre19.g750547.t1.1\r\n+17.35776\t16.51455\t17.06918\tNaN\tNaN\tNaN\tNaN\t17.24544\tNaN\tNaN\t17.10226\tNaN\t16.50288\t16.98114\t16.92381\tNaN\tNaN\t17.21457\t17.35827\tNaN\t17.02356\t17.08067\tNaN\tNaN\tNaN\t17.53306\t17.34516\t18.0164\t17.459\tNaN\tCre24.g755497.t1.1\r\n+NaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tCre36.g759647.t1.1\r\n+NaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tCre43.g760497.t1.1\r\n+19.64174\t20.08499\t20.01114\t19.5322\t19.33368\t19.69568\t19.06197\t19.54436\t19.91319\t19.62571\t19.27394\t19.73559\t19.73996\t19.82865\t19.55951\t19.92589\t18.73019\t19.52713\t19.38871\t19.2279\t19.3818\t19.1327\t18.77709\t18.99899\t19.14843\t19.0512\t19.00766\t18.63485\t18.41914\t18.61551\tCre48.g761197.t1.1\r\n+NaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tREV__Cre06.g278091.t1.1;Cre06.g278091.t1.1\r\n' |
| b |
| diff -r ba070efb6f78 -r f3fa21cda5f5 test-data/EXP11_paraR_log_properties_v1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EXP11_paraR_log_properties_v1 Fri Aug 10 15:45:44 2018 -0400 |
| b |
| @@ -0,0 +1,43 @@ +NAME GROUP EXPERIMENT +LFQ intensity 11_TP5_1 TP5 EXP +LFQ intensity 11_TP5_2 TP5 EXP +LFQ intensity 11_TP5_3 TP5 EXP +LFQ intensity 11_TP6_1 TP6 EXP +LFQ intensity 11_TP6_2 TP6 EXP +LFQ intensity 11_TP6_3 TP6 EXP +LFQ intensity 11_TP7_1 TP7 EXP +LFQ intensity 11_TP7_2 TP7 EXP +LFQ intensity 11_TP7_3 TP7 EXP +LFQ intensity 11_TP9_1 TP9 EXP +LFQ intensity 11_TP9_2 TP9 EXP +LFQ intensity 11_TP9_3 TP9 EXP +LFQ intensity 11_TP10_1 TP10 EXP +LFQ intensity 11_TP10_2 TP10 EXP +LFQ intensity 11_TP10_3 TP10 EXP +LFQ intensity 11_TP11_1 TP11 EXP +LFQ intensity 11_TP11_2 TP11 EXP +LFQ intensity 11_TP11_3 TP11 EXP +LFQ intensity 11_TP12_1 TP12 EXP +LFQ intensity 11_TP12_2 TP12 EXP +LFQ intensity 11_TP12_3 TP12 EXP +LFQ intensity 11_TP14_1 TP14 EXP +LFQ intensity 11_TP14_2 TP14 EXP +LFQ intensity 11_TP14_3 TP14 EXP +LFQ intensity 11_TP15_1 TP15 EXP +LFQ intensity 11_TP15_2 TP15 EXP +LFQ intensity 11_TP15_3 TP15 EXP +LFQ intensity 11_TP16_1 TP16 EXP +LFQ intensity 11_TP16_2 TP16 EXP +LFQ intensity 11_TP16_3 TP16 EXP +-- SEPARATE -- +NAME TIMES +TP5 -48 +TP6 -24 +TP7 0 +TP9 1 +TP10 2 +TP11 4 +TP12 6 +TP14 24 +TP15 48 +TP16 72 \ No newline at end of file |