Mercurial > repos > proteore > proteore_id_converter

annotate id_converter_UniProt.R @ 2:f8564e97ccd9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 0b1eade34b6a060e03f13ec92771694e8fc249d0-dirty
author proteore
date Fri, 24 Aug 2018 04:35:33 -0400
parents c83e45dab5c9
children f0029ded78dd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
1 # Read file and return file content as data.frame
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
2 readfile = function(filename, header) {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
3 if (header == "true") {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
4 # Read only first line of the file as header:
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
5 headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
6 #Read the data of the files (skipping the first row)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
7 file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
8 # Remove empty rows
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
9 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
10 #And assign the header to the data
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
11 names(file) <- headers
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
12 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
13 else {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
14 file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
15 # Remove empty rows
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
16 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
17 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
18 return(file)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
19 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
20
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
21 # Mapping IDs using file built from
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
22 # - HUMAN_9606_idmapping_selected.tab
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
23 # Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
24 # - nextprot_ac_list_all.txt
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
25 # Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
26 # Available databases:
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
27 # UNIPROT_AC: Uniprot accession number (e.g. P31946)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
28 # UNIPROT_ID: Uniprot identifiers (e.g 1433B_HUMAN)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
29 # GeneID_EntrezGene: Entrez gene ID (serie of digit) (e.g. 7529)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
30 # RefSeq: RefSeq (NCBI) protein (e.g. NP_003395.1; NP_647539.1; XP_016883528.1)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
31 # GI_number: GI (NCBI GI number) ID (serie of digits) assigned to each sequence record processed by NCBI (e.g; 21328448; 377656701; 67464627; 78101741)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
32 # PDB: Protein DataBank Identifiers (e.g. 2BR9:A; 3UAL:A; 3UBW:A)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
33 # GO_ID: GOterms (Gene Ontology) Identifiers (e.g. GO:0070062; GO:0005925; GO:0042470; GO:0016020; GO:0005739; GO:0005634)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
34 # PIR: Protein Information Resource ID (e.g. S34755)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
35 # OMIM: OMIM (Online Mendelian Inheritance in Man database) ID (serie of digits) (e.g: 601289)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
36 # UniGene: Unigene Identifier (e.g. Hs.643544)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
37 # Ensembl_ENSG: Ensembl gene identifiers (e.g. ENSG00000166913)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
38 # Ensembl_ENST: Ensembl transcript identifiers (e.g. ENST00000353703; ENST00000372839)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
39 # Ensembl_ENSP: Ensembl protein identifiers (e.g. ENSP00000300161; ENSP00000361930)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
40
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
41 mapping = function() {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
42 args <- commandArgs(TRUE)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
43 if(length(args)<1) {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
44 args <- c("--help")
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
45 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
46
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
47 # Help section
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
48 if("--help" %in% args) {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
49 cat("Selection and Annotation HPA
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
50 Arguments:
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
51 --ref_file: path to reference file (human_id_mapping_file.txt)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
52 --input_type: type of input (list of id or filename)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
53 --id_type: type of input IDs
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
54 --input: list of IDs (text or filename)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
55 --column_number: the column number which contains list of input IDs
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
56 --header: true/false if your file contains a header
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
57 --target_ids: target IDs to map to
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
58 --output: output filename \n")
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
59 q(save="no")
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
60 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
61
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
62 # Parse arguments
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
63 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
64 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
65 args <- as.list(as.character(argsDF$V2))
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
66 names(args) <- argsDF$V1
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
67
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
68 input_id_type = args$id_type # Uniprot, ENSG....
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
69 list_id_input_type = args$input_type # list or file
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
70 options = strsplit(args$target_ids, ",")[[1]]
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
71 output = args$output
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
72 human_id_mapping_file = args$ref_file
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
73
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
74 # Extract input IDs
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
75 if (list_id_input_type == "list") {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
76 print(args$input)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
77 list_id = trimws(strsplit(args$input, ",")[[1]])
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
78 list_id = list_id[list_id != ""] #remove empty entry
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
79 # Remove isoform accession number (e.g. "-2")
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
80 list_id = gsub("-.+", "", list_id)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
81 } else if (list_id_input_type == "file") {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
82 filename = args$input
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
83 column_number = as.numeric(gsub("c", "" ,args$column_number))
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
84 header = args$header
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
85 file_all = readfile(filename, header)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
86 list_id = trimws(gsub("[$,\xc2\xa0]","",sapply(strsplit(file_all[,column_number], ";"), "[", 1)))
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
87 # Remove isoform accession number (e.g. "-2")
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
88 list_id = gsub("-.+", "", list_id)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
89 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
90
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
91 # Extract ID maps
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
92 human_id_map = read.table(human_id_mapping_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "", quote = "")
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
93
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
94 names = c()
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
95
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
96 # Map IDs
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
97 res = matrix(nrow=length(list_id), ncol=0)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
98
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
99 for (opt in options) {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
100 names = c(names, opt)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
101 mapped = human_id_map[match(list_id, human_id_map[input_id_type][,]),][opt][,]
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
102 res = cbind(res, matrix(mapped))
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
103 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
104
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
105 # Write output
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
106 if (list_id_input_type == "list") {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
107 res = cbind(as.matrix(list_id), res)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
108 names = c(input_id_type, names)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
109 colnames(res) = names
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
110 write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
111 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
112 else if (list_id_input_type == "file") {
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
113 names(res) = options
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
114 if (all(names(file_all) == file_all[1,1:length(names(file_all))])){ #if header of file is the same as the first line of file
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
115 names(file_all)[column_number] = input_id_type
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
116 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
117 names = c(names(file_all), names)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
118 output_content = cbind(file_all, res)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
119 colnames(output_content) = names
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
120 write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
121 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
122 }
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
123
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
124 mapping()
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
125
c83e45dab5c9 planemo upload commit fa7e64b910f0f92c5f3e160536ace963c7ab0cba-dirty
proteore
parents:
diff changeset
126 #Rscript id_converter_UniProt.R "UniProt.AC" "test-data/UnipIDs.txt,c1,false" "file" "Ensembl_PRO,Ensembl,neXtProt_ID" "test-data/output.txt" ../../utils/mapping_file.txt