Merge pull request #1 from ConesaLab/1.0.1

tappAS v1.0.1
ConesaLab · May 12, 2020 · 87d7749 · 87d7749
2 parents 09fd371 + 0a99c01
commit 87d7749
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Showing 10 changed files with 738,120 additions and 145 deletions.
diff --git a/SubTabDFIResults.java b/SubTabDFIResults.java
@@ -571,10 +571,11 @@ protected Void call() throws Exception {
                                 lst.add("-r" + r);
                             }
                             lst.add("-s" + dfiParams.sigValue);
-                            lst.add("-x" + project.data.getMatrixDFIFilepath(analysisId));
                             lst.add("-c" + project.data.getDFITotalFeaturesFilepath(analysisId));
                             lst.add("-g1" + project.data.getDFITestFeaturesFilepath(analysisId));
                             lst.add("-g2" + project.data.getDFITestGenesFilepath(analysisId));
+
+                            lst.add("-x" + project.data.getMatrixDFIFilepath(analysisId));
                             lst.add("-lt" + trans);
                             lst.add("-lp" + proteins);
 

diff --git a/Tappas.java b/Tappas.java
@@ -51,7 +51,7 @@ public class Tappas extends Application {
     public static final String APP_NAME = "tappas";
     public static final int APP_MAJOR_VER = 1;
     public static final int APP_MINOR_VER = 0;
-    public static final int APP_STRREV = 0;
+    public static final int APP_STRREV = 1;
     public static final String RES_VER_FILE = "resource_v" + APP_MAJOR_VER + "." + APP_MINOR_VER + "." + APP_STRREV + ".txt";
     public static final String APP_LOCK_FILE = ".tappas.lock.prm";
     public static final String APP_PORT_PARAM = "port";

diff --git a/resources/go.obo b/resources/go.obo
diff --git a/resources/hs_ncbi_genes.tsv b/resources/hs_ncbi_genes.tsv
diff --git a/resources/mm_ncbi_genes.tsv b/resources/mm_ncbi_genes.tsv
diff --git a/resources/resource_v1.0.1.txt b/resources/resource_v1.0.1.txt
diff --git a/resources/web/contact.html b/resources/web/contact.html
@@ -51,7 +51,7 @@
         <div style="background-color:white; padding:10px;">
 
                     <b>Contact:</b>
-                    If you want to contact us to report a problem we recommend you to visit our website <a href="http://app.tappas.org/contact">http://app.tappas.org/contact</a> or send an email to <b>[email protected]</b>.
+                    If you want to contact us to report a problem we recommend you to visit our website <a href="http://app.tappas.org/contact">http://app.tappas.org/contact</a> or send an email to <b>[email protected]</b> relative to tappAS installation or errors or to <b>[email protected]</b> for tappAS functionality.
 
         </div>
         </span>

diff --git a/resources/webFiles.txt~ b/resources/webFiles.txt~
@@ -0,0 +1,9 @@
+appOverview.html
+css/web.css
+scripts/ebook.js
+scripts/maps.js
+scripts/overview.js
+scripts/scripts.js
+scripts/slides.js
+images/appLayout.png
+
diff --git a/scripts/DFI.R b/scripts/DFI.R
@@ -580,146 +580,128 @@ if(len_zero & cont_err == cont){
     lstProtein = strsplit(proteinFeatures, ",")
     dfi_total_count=read.table(file.path(inFileCount), sep="\t", header=TRUE, stringsAsFactors = F)
 
-  cat("\n1111. DFI_matrix original")
-  cat(as.character(head(result_dfi)))
-  cat("\n")
-
-  saveRDS(result_dfi, file = "D:/Pedro/Trabajo/CIPF/tappAS/tappasWorkspace/Projects/Project.0655359829.tappas/Data/DFI/my_data.rds")
-
-  cat("\nBuilding P-Values tables...")
-  dfi_matrix = unique(result_dfi[,c("gene","qValue")])
-  dfi_matrix$Feature = sapply(dfi_matrix$gene, getFeatureName)
-  dfi_matrix$Gene = sapply(dfi_matrix$gene, getGeneName)
-  dfi_matrix$DFI = ifelse(as.numeric(levels(dfi_matrix$qValue))[dfi_matrix$qValue]<=sig, "DFI", "Not DFI")
-
-  cat("\n2222. DFI_matrix original")
-  cat(as.character(head(dfi_matrix)))
-  cat("\n")
-
-  dfi_results = data.frame()
-  for(feature in unique(dfi_matrix$Feature)){
-    newRow = data.frame(Feature=feature,
-                        TotalCount=nrow(dfi_matrix[dfi_matrix$Feature==feature,]),
-                        DFICount=nrow(dfi_matrix[dfi_matrix$Feature==feature & dfi_matrix$DFI == "DFI",]),
-                        TotalAnnot=sum(dfi_total_count[dfi_total_count$Feature==feature,]$Total),
-                        Level=ifelse(feature %in% lstTrans, "Transcript","Protein"),
-                        Time="0")
-    dfi_results = rbind(dfi_results,newRow)
-  }
-
-  cat("\3333. DFI_Results primera tabla")
-  cat(as.character(dfi_results))
-  cat("\n")
-
-  dfi_results["Freq1"] = dfi_results[,"TotalCount"]/sum(dfi_results[,"TotalCount"])*100
-  dfi_results["Freq2"] = dfi_results[,"TotalAnnot"]/sum(dfi_results[,"TotalAnnot"])*100
-  dfi_results$Feature = as.character(dfi_results$Feature)
-  dfi_results = dfi_results[order(dfi_results$Feature, method = ),]
-
-  #########
-  # TEST1 #
-  #########
-
-  # feature level
-  result_utrmotif = NULL
-  for(x in unique(dfi_results$Feature)){
-    xDFI = dfi_results[dfi_results$Feature==x,]$DFICount
-    xANNOT = dfi_results[dfi_results$Feature==x,]$TotalAnnot-xDFI
-    allDFI = sum(dfi_results[dfi_results$Feature!=x,]$DFICount)
-    allANNOT = sum(dfi_results[dfi_results$Feature!=x, ]$TotalAnnot)-allDFI
-
-    tbDFI <- matrix(c(xDFI,xANNOT,allDFI,allANNOT),ncol=2,byrow=TRUE)
-    colnames(tbDFI) <- c("DFI","ANNOT-DFI")
-    rownames(tbDFI) <- c("X","ALL")
-    tbDFI <- as.table(tbDFI)
-
-    result_utrmotif = rbind(result_utrmotif, c(x,fisher.test(x = tbDFI, alternative="less")$p.value, as.character(tbDFI)))
-  }
-  result_utrmotif_df = data.frame(result_utrmotif, stringsAsFactors = F)
-  result_utrmotif_df$X2 = as.numeric(result_utrmotif_df$X2)
-  result_utrmotif_df$adj = p.adjust(result_utrmotif_df$X2, method = "hochberg")
-  result_utrmotif_df = result_utrmotif_df[order(result_utrmotif_df$X1),]
-  colnames(result_utrmotif_df) = c("Feature","P-Value","feat_DFI","all_DFI","feat_ANNOT-DFI","all_ANNOT-DFI", "Adj.P-Value")
-  result_utrmotif_df$`P-Value` = signif(result_utrmotif_df$`P-Value`, digits = 5)
-  result_utrmotif_df$`Adj.P-Value` = signif(result_utrmotif_df$`Adj.P-Value`, digits = 5)
-
-  cat("\4444. DFI_Results segunda tabla")
-  cat(as.character(result_utrmotif_df))
-  cat("\n")
-
-  ##############
-  # SAVE TESTS #
-  ##############
-
-  write.table(result_utrmotif_df, file = outputTestFeatures, quote = FALSE, col.names = TRUE, row.names = FALSE, sep = "\t")
-
-  #########
-  # TEST2 #
-  #########
-
-  # gene level
-  cat("\nWriting DFI Test2 file...\n")
+    cat("\nBuilding P-Values tables...")
+    dfi_matrix = unique(result_dfi[,c("gene","qValue")])
+    dfi_matrix$Feature = sapply(dfi_matrix$gene, getFeatureName)
+    dfi_matrix$Gene = sapply(dfi_matrix$gene, getGeneName)
+    dfi_matrix$DFI = ifelse(as.numeric(levels(dfi_matrix$qValue))[dfi_matrix$qValue]<=sig, "DFI", "Not DFI")
+
+    dfi_results = data.frame()
+    for(feature in unique(dfi_matrix$Feature)){
+      newRow = data.frame(Feature=feature,
+                          TotalCount=nrow(dfi_matrix[dfi_matrix$Feature==feature,]),
+                          DFICount=nrow(dfi_matrix[dfi_matrix$Feature==feature & dfi_matrix$DFI == "DFI",]),
+                          TotalAnnot=sum(dfi_total_count[dfi_total_count$Feature==feature,]$Total),
+                          Level=ifelse(feature %in% lstTrans, "Transcript","Protein"),
+                          Time="0")
+      dfi_results = rbind(dfi_results,newRow)
+    }
 
-  res_genes = NULL
-  dfi_matrix_genes = unique(dfi_matrix[,c("Gene","Feature","DFI")])
-  for(gene in unique(dfi_matrix_genes$Gene)){
-    for(feature in unique(dfi_matrix_genes[dfi_matrix_genes$Gene == gene,]$Feature)){
-      submatrix = dfi_matrix_genes[dfi_matrix_genes$Gene == gene & dfi_matrix_genes$Feature == feature,]
-      if(nrow(submatrix)>1) #a DFI and Not DFI
-        res_genes = rbind(res_genes, submatrix[submatrix$DFI == "DFI",])
-      else
-        res_genes = rbind(res_genes, submatrix)
+    dfi_results["Freq1"] = dfi_results[,"TotalCount"]/sum(dfi_results[,"TotalCount"])*100
+    dfi_results["Freq2"] = dfi_results[,"TotalAnnot"]/sum(dfi_results[,"TotalAnnot"])*100
+    dfi_results$Feature = as.character(dfi_results$Feature)
+    dfi_results = dfi_results[order(dfi_results$Feature, method = ),]
+
+    #########
+    # TEST1 #
+    #########
+
+    # feature level
+    result_utrmotif = NULL
+    for(x in unique(dfi_results$Feature)){
+      xDFI = dfi_results[dfi_results$Feature==x,]$DFICount
+      xANNOT = dfi_results[dfi_results$Feature==x,]$TotalAnnot-xDFI
+      allDFI = sum(dfi_results[dfi_results$Feature!=x,]$DFICount)
+      allANNOT = sum(dfi_results[dfi_results$Feature!=x, ]$TotalAnnot)-allDFI
+
+      tbDFI <- matrix(c(xDFI,xANNOT,allDFI,allANNOT),ncol=2,byrow=TRUE)
+      colnames(tbDFI) <- c("DFI","ANNOT-DFI")
+      rownames(tbDFI) <- c("X","ALL")
+      tbDFI <- as.table(tbDFI)
+
+      result_utrmotif = rbind(result_utrmotif, c(x,fisher.test(x = tbDFI, alternative="less")$p.value, as.character(tbDFI)))
+    }
+    result_utrmotif_df = data.frame(result_utrmotif, stringsAsFactors = F)
+    result_utrmotif_df$X2 = as.numeric(result_utrmotif_df$X2)
+    result_utrmotif_df$adj = p.adjust(result_utrmotif_df$X2, method = "hochberg")
+    result_utrmotif_df = result_utrmotif_df[order(result_utrmotif_df$X1),]
+    colnames(result_utrmotif_df) = c("Feature","P-Value","feat_DFI","all_DFI","feat_ANNOT-DFI","all_ANNOT-DFI", "Adj.P-Value")
+    result_utrmotif_df$`P-Value` = signif(result_utrmotif_df$`P-Value`, digits = 5)
+    result_utrmotif_df$`Adj.P-Value` = signif(result_utrmotif_df$`Adj.P-Value`, digits = 5)
+
+    ##############
+    # SAVE TESTS #
+    ##############
+
+    write.table(result_utrmotif_df, file = outputTestFeatures, quote = FALSE, col.names = TRUE, row.names = FALSE, sep = "\t")
+
+    #########
+    # TEST2 #
+    #########
+
+    # gene level
+    cat("\nWriting DFI Test2 file...\n")
+
+    res_genes = NULL
+    dfi_matrix_genes = unique(dfi_matrix[,c("Gene","Feature","DFI")])
+    for(gene in unique(dfi_matrix_genes$Gene)){
+      for(feature in unique(dfi_matrix_genes[dfi_matrix_genes$Gene == gene,]$Feature)){
+        submatrix = dfi_matrix_genes[dfi_matrix_genes$Gene == gene & dfi_matrix_genes$Feature == feature,]
+        if(nrow(submatrix)>1) #a DFI and Not DFI
+          res_genes = rbind(res_genes, submatrix[submatrix$DFI == "DFI",])
+        else
+          res_genes = rbind(res_genes, submatrix)
+      }
     }
-  }
 
-  dfi_results = data.frame()
-  for(feature in unique(res_genes$Feature)){
-    newRow = data.frame(Feature=feature,
-                        TotalCount=nrow(res_genes[res_genes$Feature==feature,]),
-                        DFICount=nrow(res_genes[res_genes$Feature==feature & res_genes$DFI == "DFI",]),
-                        TotalAnnot=sum(dfi_total_count[dfi_total_count$Feature==feature,]$ByGenes),
-                        Level=ifelse(feature %in% lstTrans, "Transcript","Protein"),
-                        Time="0")
-    dfi_results = rbind(dfi_results,newRow)
-  }
+    dfi_results = data.frame()
+    for(feature in unique(res_genes$Feature)){
+      newRow = data.frame(Feature=feature,
+                          TotalCount=nrow(res_genes[res_genes$Feature==feature,]),
+                          DFICount=nrow(res_genes[res_genes$Feature==feature & res_genes$DFI == "DFI",]),
+                          TotalAnnot=sum(dfi_total_count[dfi_total_count$Feature==feature,]$ByGenes),
+                          Level=ifelse(feature %in% lstTrans, "Transcript","Protein"),
+                          Time="0")
+      dfi_results = rbind(dfi_results,newRow)
+    }
 
-  dfi_results["Freq1"] = dfi_results[,"TotalCount"]/sum(dfi_results[,"TotalCount"])*100
-  dfi_results["Freq2"] = dfi_results[,"TotalAnnot"]/sum(dfi_results[,"TotalAnnot"])*100
-  dfi_results$Feature = as.character(dfi_results$Feature)
-  dfi_results = dfi_results[order(dfi_results$Feature, method = ),]
-
-  #########
-  # TEST2 #
-  #########
-
-  # gene level
-  result_utrmotif = NULL
-  for(x in unique(dfi_results$Feature)){
-    xDFI = dfi_results[dfi_results$Feature==x,]$DFICount
-    xANNOT = dfi_results[dfi_results$Feature==x,]$TotalAnnot-xDFI
-    allDFI = sum(dfi_results[dfi_results$Feature!=x,]$DFICount)
-    allANNOT = sum(dfi_results[dfi_results$Feature!=x, ]$TotalAnnot)-allDFI
-
-    tbDFI <- matrix(c(xDFI,xANNOT,allDFI,allANNOT),ncol=2,byrow=TRUE)
-    colnames(tbDFI) <- c("DFI","ANNOT-DFI")
-    rownames(tbDFI) <- c("X","ALL")
-    tbDFI <- as.table(tbDFI)
-
-    result_utrmotif = rbind(result_utrmotif, c(x,fisher.test(x = tbDFI, alternative="less")$p.value, as.character(tbDFI)))
-  }
-  result_utrmotif_gene = data.frame(result_utrmotif, stringsAsFactors = F)
-  result_utrmotif_gene$X2 = as.numeric(result_utrmotif_gene$X2)
-  result_utrmotif_gene$adj = p.adjust(result_utrmotif_gene$X2, method = "hochberg")
-  result_utrmotif_gene = result_utrmotif_gene[order(result_utrmotif_gene$X1),]
-  colnames(result_utrmotif_gene) = c("Feature","P-Value","feat_DFI","all_DFI","feat_ANNOT-DFI","all_ANNOT-DFI", "Adj.P-Value")
-  result_utrmotif_gene$`P-Value` = signif(result_utrmotif_gene$`P-Value`, digits = 5)
-  result_utrmotif_gene$`Adj.P-Value` = signif(result_utrmotif_gene$`Adj.P-Value`, digits = 5)
-
-  ##############
-  # SAVE TESTS #
-  ##############
-
-  write.table(result_utrmotif_gene, file = outputTestGenes, quote = FALSE, col.names = TRUE, row.names = FALSE, sep = "\t")
+    dfi_results["Freq1"] = dfi_results[,"TotalCount"]/sum(dfi_results[,"TotalCount"])*100
+    dfi_results["Freq2"] = dfi_results[,"TotalAnnot"]/sum(dfi_results[,"TotalAnnot"])*100
+    dfi_results$Feature = as.character(dfi_results$Feature)
+    dfi_results = dfi_results[order(dfi_results$Feature, method = ),]
+
+    #########
+    # TEST2 #
+    #########
+
+    # gene level
+    result_utrmotif = NULL
+    for(x in unique(dfi_results$Feature)){
+      xDFI = dfi_results[dfi_results$Feature==x,]$DFICount
+      xANNOT = dfi_results[dfi_results$Feature==x,]$TotalAnnot-xDFI
+      allDFI = sum(dfi_results[dfi_results$Feature!=x,]$DFICount)
+      allANNOT = sum(dfi_results[dfi_results$Feature!=x, ]$TotalAnnot)-allDFI
+
+      tbDFI <- matrix(c(xDFI,xANNOT,allDFI,allANNOT),ncol=2,byrow=TRUE)
+      colnames(tbDFI) <- c("DFI","ANNOT-DFI")
+      rownames(tbDFI) <- c("X","ALL")
+      tbDFI <- as.table(tbDFI)
+
+      result_utrmotif = rbind(result_utrmotif, c(x,fisher.test(x = tbDFI, alternative="less")$p.value, as.character(tbDFI)))
+    }
+    result_utrmotif_gene = data.frame(result_utrmotif, stringsAsFactors = F)
+    result_utrmotif_gene$X2 = as.numeric(result_utrmotif_gene$X2)
+    result_utrmotif_gene$adj = p.adjust(result_utrmotif_gene$X2, method = "hochberg")
+    result_utrmotif_gene = result_utrmotif_gene[order(result_utrmotif_gene$X1),]
+    colnames(result_utrmotif_gene) = c("Feature","P-Value","feat_DFI","all_DFI","feat_ANNOT-DFI","all_ANNOT-DFI", "Adj.P-Value")
+    result_utrmotif_gene$`P-Value` = signif(result_utrmotif_gene$`P-Value`, digits = 5)
+    result_utrmotif_gene$`Adj.P-Value` = signif(result_utrmotif_gene$`Adj.P-Value`, digits = 5)
+
+    ##############
+    # SAVE TESTS #
+    ##############
+
+    write.table(result_utrmotif_gene, file = outputTestGenes, quote = FALSE, col.names = TRUE, row.names = FALSE, sep = "\t")
 
     cat("\nAll done.\n")
 }