Removed some redudante output messages, reviewed code for unneccessar…

…y comments
imgag · Oct 8, 2018 · b06e4fa · b06e4fa
1 parent 9cfc865
commit b06e4fa
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Showing 3 changed files with 3 additions and 44 deletions.
diff --git a/somatic/firstStep.R b/somatic/firstStep.R
@@ -64,18 +64,6 @@ option_list = list(
 opt_parser = OptionParser(option_list=option_list);
 opt = parse_args(opt_parser);
 
-### TESTING PART
-# opt$bed = "/Users/gdemidov/Tuebingen/somatic_CNVs/Somatic/ssSC_v2.annotated.bed"
-# opt$tumor = "/Users/gdemidov/Tuebingen/somatic_CNVs/Somatic/tumor2.cov"
-# opt$normal = "/Users/gdemidov/Tuebingen/somatic_CNVs/Somatic/normal2.cov"
-# opt$colNum = 4
-# opt$pair = "/Users/gdemidov/Tuebingen/somatic_CNVs/Somatic/pairs.txt"
-# opt$out = "/Users/gdemidov/Tuebingen/clinCNV_dev/results"
-# opt$folderWithScript = "/Users/gdemidov/Tuebingen/clinCNV_dev/ClinCNV/somatic"
-# opt$reanalyseCohort = F
-# opt$bedOfftarget = "/Users/gdemidov/Tuebingen/somatic_CNVs/Somatic/offtaget_annotated_ssSC_v2_2015_01_26.bed"
-# opt$tumorOfftarget = "/Users/gdemidov/Tuebingen/somatic_CNVs/Somatic/offtarget2.txt"
-# opt$normalOfftarget = "/Users/gdemidov/Tuebingen/somatic_CNVs/Somatic/offtarget2.txt"
 
 ### PLOTTING OF PICTURES (DOES NOT REALLY NECESSARY IF YOU HAVE IGV SEGMENTS)
 plottingOfPNGs = F
@@ -656,9 +644,6 @@ for (sam_no in 1:ncol(matrixOfLogFold)) {
         }
 
 
-
-
-
         if(opt$debug) {
           print(found_CNVs)
           print(l)
@@ -711,7 +696,9 @@ for (sam_no in 1:ncol(matrixOfLogFold)) {
     fileConn<-file(fileToOut)
     writeLines(c(paste("##"," QC ", 0, collapse = " ")), fileConn)
     close(fileConn)
-    print(found_CNVs_total)
+    if(opt$debug) {
+        print(found_CNVs_total)
+    }
     write.table(found_CNVs_total, file = fileToOut, quote=F, row.names = F, sep="\t", append = T)	
   }  
 }
diff --git a/somatic/generalHelpers.R b/somatic/generalHelpers.R
@@ -264,29 +264,6 @@ find_all_CNVs <- function(minimum_length_of_CNV, threshold, price_per_tile, init
           matrix_of_likeliks[k,] = 0
         }
 
-      # if (found_CNV[4] >= 2 & found_CNV[4] <= 4) {
-      #   for (k in found_CNV[2]:found_CNV[3]) {
-      #     matrix_of_likeliks[k,found_CNV[4]] = matrix_of_likeliks[k,current_region_to_look_for_CNVs[4]]
-      #   }
-      # } else {
-      #   if (found_CNV[4] == 1) {
-      #     # replace borders as they are heterozygous deletions
-      #     matrix_of_likeliks[max((found_CNV[2] - 1), start), 1] = matrix_of_likeliks[max((found_CNV[2] - 1), start), 2]
-      #     matrix_of_likeliks[min((found_CNV[3] + 1), end), 1] = matrix_of_likeliks[min((found_CNV[3] + 1), end), 2]
-      #   }
-      #   if (found_CNV[4] > 4) {
-      #     # replace borders as they are heterozygous duplications
-      #     matrix_of_likeliks[max((found_CNV[2] - 1), start), found_CNV[4]] = matrix_of_likeliks[max((found_CNV[2] - 1), start), 4]
-      #     matrix_of_likeliks[min((found_CNV[3] + 1), end), found_CNV[4]] = matrix_of_likeliks[min((found_CNV[3] + 1), end), 4]
-      #   }
-      #   found_CNV_with_changed = find_one_CNV(start, end, current_region_to_look_for_CNVs[4], threshold, matrix_of_likeliks, minimum_length_of_CNV)
-      #   if (found_CNV_with_changed[3] == found_CNV[3] & found_CNV_with_changed[2] == found_CNV[2]) {
-      #     # evaluate_segment_further = F
-      #     for (k in max((found_CNV[2] - 1), start):min((found_CNV[3] + 1), end)) {
-      #       matrix_of_likeliks[k,found_CNV[4]] = matrix_of_likeliks[k,current_region_to_look_for_CNVs[4]]
-      #     }
-      #   }
-      # }
       matrix_for_calculations <- -matrix_of_likeliks[start:end,] + matrix_of_likeliks[start:end, initial_state]
       if (!is.null(nrow(matrix_for_calculations))) {
         matrix_for_calculations <- apply(matrix_for_calculations, 2, sum)
@@ -350,7 +327,6 @@ outputSegmentsAndDotsFromListOfCNVs <- function(toyBedFile, foundCNVs, startOfCh
     ### MAKE ANNOTATION TO TRACK FILES
     makeTrackAnnotation <- function(fileName) {
       if (!file.exists(fileName)) {
-        print("WE CREATE FILE")
         file.create(fileName)
         fileConn<-file(fileName)
         writeLines(c("#type=GENE_EXPRESSION",

diff --git a/somatic/helpersSomatic.R b/somatic/helpersSomatic.R
@@ -24,10 +24,6 @@ determineSDsOfSomaticSample <- function(x) {
   else {
        for (i in 2:length(bordersOfChroms)) {
          valuesBetweenBorders <- x[bordersOfChroms[i-1]:bordersOfChroms[i]]
-         #valuesBetweenDelAndDup <- which(valuesBetweenBorders > -1 & valuesBetweenBorders < log2(3/2))
-         #if (length(valuesBetweenDelAndDup) > 0.5 * length(valuesBetweenBorders)) {
-        #    valuesBetweenBorders <- valuesBetweenBorders[valuesBetweenDelAndDup]
-        # }
          sdsS[i] = Sn(valuesBetweenBorders)
       }
   }