Mercurial > repos > proteore > proteore_goprofiles

comparison goprofiles.R @ 4:715002a394ec draft

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planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
author proteore
date Fri, 23 Mar 2018 10:47:17 -0400
parents 58a8ddd58dde
children 781072a65600
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3:ed226f0e5625 4:715002a394ec
1 # Load necessary libraries 1 # Load necessary libraries
2 library(org.Hs.eg.db) 2 library(org.Hs.eg.db)
3 library(goProfiles) 3 library(goProfiles)
4 4
5 # Read file and return file content as data.frame? 5 # Read file and return file content as data.frame
6 readfile = function(filename, header) { 6 readfile = function(filename, header) {
7 if (header == "true") { 7 if (header == "true") {
8 # Read only the first line of the files as data (without headers): 8 # Read only first line of the file as header:
9 headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE) 9 headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
10 #Read the data of the files (skipping the first row): 10 #Read the data of the files (skipping the first row)
11 file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE) 11 file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
12 # Remove empty rows 12 # Remove empty rows
13 file <- file[!apply(is.na(file) | file == "", 1, all),] 13 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
14 #And assign the headers of step two to the data: 14 #And assign the header to the data
15 names(file) <- headers 15 names(file) <- headers
16 } 16 }
17 else { 17 else {
18 file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE) 18 file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
19 # Remove empty rows
20 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
19 } 21 }
20 return(file) 22 return(file)
21 } 23 }
22 24
23 getprofile = function(ids, id_type, level, duplicate) { 25 getprofile = function(ids, id_type, level, duplicate) {
173 args <- as.list(as.character(argsDF$V2)) 175 args <- as.list(as.character(argsDF$V2))
174 names(args) <- argsDF$V1 176 names(args) <- argsDF$V1
175 177
176 input_type = args$input_type 178 input_type = args$input_type
177 if (input_type == "text") { 179 if (input_type == "text") {
178 input = strsplit(args$input, " ")[[1]] 180 input = strsplit(args$input, "[ \t\n]+")[[1]]
179 } 181 }
180 else if (input_type == "file") { 182 else if (input_type == "file") {
181 filename = args$input 183 filename = args$input
182 ncol = args$ncol 184 ncol = args$ncol
183 # Check ncol 185 # Check ncol