Mercurial > repos > proteore > proteore_goprofiles

comparison goprofiles.R @ 6:6afe8166a9a4 draft

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planemo upload commit 4e898239997b7ef266b1d0ce0a4c7cdec31b4ecd-dirty
author proteore
date Fri, 21 Sep 2018 09:23:38 -0400
parents 781072a65600
children 3e138d54c105
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5:781072a65600 6:6afe8166a9a4
1 options(warn=-1) #TURN OFF WARNINGS !!!!!!
2
1 # Load necessary libraries 3 # Load necessary libraries
2 library(goProfiles,quietly = TRUE) 4 suppressMessages(library(goProfiles,quietly = TRUE))
3 5
4 # Read file and return file content as data.frame 6 # Read file and return file content as data.frame
5 readfile = function(filename, header) { 7 readfile = function(filename, header) {
6 if (header == "true") { 8 if (header == "true") {
7 # Read only first line of the file as header: 9 # Read only first line of the file as header:
21 return(file) 23 return(file)
22 } 24 }
23 25
24 check_ids <- function(vector,type) { 26 check_ids <- function(vector,type) {
25 uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$" 27 uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"
26 entrez_id = "^'[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$" 28 entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
27 if (type == "Entrez"){ 29 if (type == "Entrez"){
28 return(grepl(entrez_id,vector)) 30 return(grepl(entrez_id,vector))
29 } else if (type == "UniProt") { 31 } else if (type == "UniProt") {
30 return(grepl(uniprot_pattern,vector)) 32 return(grepl(uniprot_pattern,vector))
31 } 33 }
212 } 214 }
213 header = args$header 215 header = args$header
214 # Get file content 216 # Get file content
215 file = readfile(filename, header) 217 file = readfile(filename, header)
216 # Extract Protein IDs list 218 # Extract Protein IDs list
217 input = c() 219 input = unlist(strsplit(file[,ncol],";"))
218 for (row in as.character(file[,ncol])) { 220 input = input [which(!is.na(input))]
219 input = c(input, strsplit(row, ";")[[1]][1])
220 }
221 } 221 }
222 222
223 if (! any(check_ids(input,id_type))){ 223 if (! any(check_ids(input,id_type))){
224 stop(paste(id_type,"not found in your ids list, please check your IDs in input or the selected column of your input file")) 224 stop(paste(id_type,"not found in your ids list, please check your IDs in input or the selected column of your input file"))
225 } 225 }