Mercurial > repos > proteore > proteore_prot_features
annotate protein_features.R @ 6:fc0118aa432a draft
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author | proteore |
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date | Tue, 20 Mar 2018 11:13:49 -0400 |
parents | 867d47ff782c |
children | af7089d1c7c0 |
rev | line source |
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1 # Read file and return file content as data.frame |
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2 readfile = function(filename, header) { |
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3 if (header == "true") { |
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4 # Read only first line of the file as header: |
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5 headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "") |
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6 #Read the data of the files (skipping the first row) |
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7 file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "") |
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8 # Remove empty rows |
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9 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] |
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10 #And assign the header to the data |
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11 names(file) <- headers |
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12 } |
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13 else { |
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14 file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "") |
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15 # Remove empty rows |
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16 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] |
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17 } |
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18 return(file) |
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19 } |
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20 |
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21 protein_features = function() { |
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22 args <- commandArgs(TRUE) |
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23 if(length(args)<1) { |
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24 args <- c("--help") |
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25 } |
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26 |
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27 # Help section |
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28 if("--help" %in% args) { |
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29 cat("Selection and Annotation HPA |
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30 Arguments: |
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31 --inputtype: type of input (list of id or filename) |
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32 --input: input |
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33 --nextprot: path to nextprot information file |
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34 --column: the column number which you would like to apply... |
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35 --header: true/false if your file contains a header |
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36 --type: the type of input IDs (UniProt/EntrezID) |
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37 --argsP1: IsoPoint,SeqLength,MW |
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38 --argsP2: Chr,SubcellLocations |
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39 --argsP3: Diseases |
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40 --output: text output filename \n") |
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41 q(save="no") |
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42 } |
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43 |
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44 # Parse arguments |
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45 parseArgs <- function(x) strsplit(sub("^--", "", x), "=") |
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46 argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) |
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47 args <- as.list(as.character(argsDF$V2)) |
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48 names(args) <- argsDF$V1 |
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49 |
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50 inputtype = args$inputtype |
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51 if (inputtype == "copypaste") { |
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52 input = strsplit(args$input, "[ \t\n]+")[[1]] |
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53 } |
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54 else if (inputtype == "tabfile") { |
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55 filename = args$input |
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56 ncol = args$column |
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57 # Check ncol |
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58 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) { |
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59 stop("Please enter an integer for level") |
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60 } |
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61 else { |
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62 ncol = as.numeric(gsub("c", "", ncol)) |
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63 } |
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64 header = args$header |
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65 # Get file content |
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66 file = readfile(filename, header) |
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67 # Extract Protein IDs list |
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68 input = c() |
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69 for (row in as.character(file[,ncol])) { |
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70 input = c(input, strsplit(row, ";")[[1]][1]) |
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71 } |
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72 } |
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73 |
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74 # Read reference file |
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75 nextprot_file = args$nextprot |
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76 nextprot = read.table(nextprot_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "", quote = "") |
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77 |
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78 # Parse arguments |
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79 typeid = args$type |
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80 P1_args = strsplit(args$argsP1, ",")[[1]] |
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81 P2_args = strsplit(args$argsP2, ",")[[1]] |
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82 P3_args = strsplit(args$argsP3, ",")[[1]] |
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83 output = args$output |
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84 |
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85 # Change the sample ids if they are uniprot ids to be able to match them with |
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86 # Nextprot data |
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87 if (typeid=="uniprot"){ |
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88 input = gsub("^","NX_",input) |
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89 } |
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90 |
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91 # Select user input protein ids in nextprot |
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92 if ((length(input[input %in% nextprot[,1]]))==0){ |
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93 write.table("None of the input ids are can be found in Nextprot",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE) |
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94 } else { |
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95 names = c() |
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96 res = matrix(nrow=length(input), ncol=0) |
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97 |
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98 # Get information from neXtProt |
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99 if (length(P1_args)>0) { |
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100 for (arg in P1_args) { |
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101 names = c(names, arg) |
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102 info = nextprot[match(input, nextprot["NextprotID"][,]),][arg][,] |
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103 res = cbind(res, info) |
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104 } |
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105 } |
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106 if (length(P2_args)>0) { |
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107 for (arg in P2_args) { |
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108 names = c(names, arg) |
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109 info = nextprot[match(input, nextprot["NextprotID"][,]),][arg][,] |
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110 res = cbind(res, info) |
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111 } |
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112 } |
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113 if (length(P3_args)>0) { |
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114 for (arg in P3_args) { |
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115 names = c(names, arg) |
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116 info = nextprot[match(input, nextprot["NextprotID"][,]),][arg][,] |
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117 res = cbind(res, info) |
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118 } |
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119 } |
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120 --inputtype="tabfile" --input="Galaxy50-[ID_Converter_on_data_47].tabular" --header='true' --natlas="proteinatlas.csv" --column='c7' --select='Gene,Gene.description,Evidence,RNA.tissue.category,Reliability.IH,TPM.max.in.non.specific' --output="test.txt" |
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121 |
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122 # Write output |
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123 if (inputtype == "copypaste") { |
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124 res = cbind(as.matrix(input), res) |
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125 names = c(typeid, names) |
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126 colnames(res) = names |
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127 write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE) |
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128 } |
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129 else if (inputtype == "tabfile") { |
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130 names = c(names(file), names) |
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131 output_content = cbind(file, res) |
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132 colnames(output_content) = names |
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133 write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE) |
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134 } |
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135 } |
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136 |
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137 } |
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138 protein_features() |