Mercurial > repos > proteore > proteore_prot_features

annotate protein_features.R @ 8:2e53ba3b1697 draft

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planemo upload commit cb952d34dce3fd5cd7baa6f69fdaae3a1174d12e-dirty
author proteore
date Fri, 23 Mar 2018 10:37:36 -0400
parents af7089d1c7c0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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
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121 # Write output
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122 if (inputtype == "copypaste") {
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123 res = cbind(as.matrix(input), res)
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124 names = c(typeid, names)
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125 colnames(res) = names
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126 write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE)
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127 }
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128 else if (inputtype == "tabfile") {
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129 names = c(names(file), names)
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130 output_content = cbind(file, res)
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131 colnames(output_content) = names
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132 write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
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133 }
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134 }
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135
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136 }
5
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137 protein_features()