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1 if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
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2 args=commandArgs(TRUE)
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3
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4 # get args names and values
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5 args_values=strsplit(args,'=')
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6 args_names=unlist(lapply(args_values,function(arg) arg[1]))
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7 names(args_values)=args_names
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8 args_values=lapply(args_values,function(arg) arg[2])
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9 # read filenames
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10 outrdata=args_values$outrdata
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11 outregions=args_values$outregions
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12 outfeatures=args_values$outfeatures
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13 outpdf=args_values$outpdf
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14 regionspaths=unlist(strsplit(args_values$regionspaths,'\\|'))
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15 if("regionsheaderfile" %in% args_names){
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16 # the file regionsheaderfile must contain as first column the (unique) regionsfilenames,
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17 # as second column the corresponding ids and as third column the names
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18 tryCatch({
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19 regionsheader=read.delim(args_values$regionsheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
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20 regionsfilenames=unlist(strsplit(args_values$regionsfilenames,'\\|'))
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21 if(length(setdiff(regionsfilenames,row.names(regionsheader)))) {
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22 write("IWTomics message: Not all region files are present in the first column of header file for regions.", stderr())
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23 quit(save="no", status=11)
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24 }
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25 id_regions=regionsheader[regionsfilenames,1]
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26 name_regions=regionsheader[regionsfilenames,2]
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27 }, error = function(err) {
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28 write("IWTomics message: An error has occurred reading the header file for regions. Please try again.", stderr())
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29 quit(save="no", status=10) #error on header file
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30 })
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31 }else{
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32 eval(parse(text=args[[which(args_names=='regionsgalaxyids')]]))
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33 id_regions=paste0('data_',regionsgalaxyids)
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34 name_regions=paste0('data_',regionsgalaxyids)
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35 }
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36 featurespaths=unlist(strsplit(args_values$featurespaths,'\\|'))
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37 if("featuresheaderfile" %in% args_names){
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38 # the file featuresheaderfile must contain as first column the (unique) featuresfilenames,
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39 # as second column the corresponding ids and as third column the names
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40 tryCatch({
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41 featuresheader=read.delim(args_values$featuresheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
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42 featuresfilenames=unlist(strsplit(args_values$featuresfilenames,'\\|'))
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43 if(length(setdiff(featuresfilenames,row.names(featuresheader)))) {
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44 write("IWTomics message: Not all feature files are present in the first column of header file for features.", stderr())
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45 quit(save="no", status=21)
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46 }
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47 id_features=featuresheader[featuresfilenames,1]
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48 name_features=featuresheader[featuresfilenames,2]
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49 }, error = function(err) {
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50 write("IWTomics message: An error has occurred reading the header file for features. Please try again.", stderr())
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51 quit(save="no", status=20) #error on header file
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52 })
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53 }else{
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54 eval(parse(text=args[[which(args_names=='featuresgalaxyids')]]))
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55 id_features=paste0('data_',featuresgalaxyids)
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56 name_features=paste0('data_',featuresgalaxyids)
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57 }
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58 # read parameters (from smoothing on)
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59 i_smoothing=which(args_names=='smoothing')
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60 for(i in i_smoothing:length(args)){
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61 eval(parse(text=args[[i]]))
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62 }
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63
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64 # load data
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65 tryCatch({
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66 regionsFeatures=IWTomicsData(regionspaths,featurespaths,alignment,
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67 id_regions,name_regions,id_features,name_features,start.are.0based=start.are.0based)
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68 }, error = function(err) {
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69 if(grepl('invalid format',err$message)){
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70 write("IWTomics message: Not enough columns in input file.", stderr())
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71 quit(save="no", status=31) # error, not enough columns in input file
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72 }else if(grepl('duplicated regions',err$message)){
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73 write("IWTomics message: Duplicated regions in region file.", stderr())
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74 quit(save="no", status=32) # error, duplicated regions in region file
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75 }else if(grepl('duplicated windows',err$message)){
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76 write("IWTomics message: Duplicated windows in feature file.", stderr())
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77 quit(save="no", status=33) # error, duplicated windows in feature file
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78 }else if(grepl('overlapping windows',err$message)){
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79 write("IWTomics message: Overlapping windows in feature file.", stderr())
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80 quit(save="no", status=34) # error, overlapping windows in feature file
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81 }else if(grepl('not all regions in datasets',err$message)){
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82 write("IWTomics message: Windows in feature files do not cover all regions in region files.", stderr())
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83 quit(save="no", status=35) # error, windows in feature files do not cover all regions in region files
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84 }else if(grepl('ifferent size windows',err$message)){
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85 write("IWTomics message: All windows in a feature file must have the same size.", stderr())
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86 quit(save="no", status=36) # error, all windows in a feature files must have the same size
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87 }
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88 #error loading data
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89 write("IWTomics message: An error has occurred reading the data. Please try again.", stderr())
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90 quit(save="no", status=30)
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91 })
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92
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93 # smooth data
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94 if(smoothing!='no'){
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95 tryCatch({
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96 if(smoothing=='locpoly'){
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97 dist_knots=10
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98 }else if(smoothing=='kernel'){
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99 degree=3
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100 dist_knots=10
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101 }else if(smoothing=='splines'){
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102 bandwidth=5
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103 }
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104 if(alignment=='scale'){
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105 if(scale==0){
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106 regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
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107 bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
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108 }else{
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109 regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
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110 bandwidth=bandwidth,degree=degree,dist_knots=dist_knots,scale_grid=scale)
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111 }
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112 }else{
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113 regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
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114 bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
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115 }
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116 }, error = function(err) {
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117 write("IWTomics message: An error has occurred smoothing the data. Please try again.", stderr())
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118 quit(save="no", status=40) #error on smoothing
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119 })
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120 }
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121
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122 # plot data
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123 pdf(outpdf,width=10,height=8)
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124 if(plottype=='boxplot'){
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125 # fix repeated probs
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126 probs=sort(unique(probs))
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127 }else{
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128 probs=c(0.25,0.5,0.75)
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129 }
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130 plot(regionsFeatures,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
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131 dev.off()
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132
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133 # create output
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134 #write.table(cbind(unlist(strsplit(args_values$regionsfilenames,'\\|')),idRegions(regionsFeatures),nameRegions(regionsFeatures)),
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135 #file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
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136 write.table(as.data.frame(t(idRegions(regionsFeatures))),file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
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137 #write.table(cbind(unlist(strsplit(args_values$featuresfilenames,'\\|')),idFeatures(regionsFeatures),nameFeatures(regionsFeatures)),
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138 #file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
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139 write.table(as.data.frame(t(idFeatures(regionsFeatures))),file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
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140 save(regionsFeatures,file=outrdata)
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141 }else{
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142 write("IWTomics message: Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
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143 quit(save="no", status=255)
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144 } |
