Mercurial > repos > proteore > proteore_pathview_mapping

comparison PathView.R @ 7:b617d4bbebf8 draft

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planemo upload commit 41ba6f74dfad14f894dbe396fc765893b971b5ae-dirty
author proteore
date Mon, 27 Aug 2018 11:21:34 -0400
parents 097bb3ed2b4d
children 33c9bd75882a
comparison
equal deleted inserted replaced
6:059f17f98ab5 7:b617d4bbebf8
61 ./PathView.R --input 'input.csv' --pathway_id '05412' --id_type 'uniprotID' --id_column 'c1' --header TRUE \n\n") 61 ./PathView.R --input 'input.csv' --pathway_id '05412' --id_type 'uniprotID' --id_column 'c1' --header TRUE \n\n")
62 62
63 q(save="no") 63 q(save="no")
64 } 64 }
65 65
66
67 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda")
68 #load("/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda")
69 parseArgs <- function(x) strsplit(sub("^--", "", x), "=") 66 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
70 argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) 67 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
71 args <- as.list(as.character(argsDF$V2)) 68 args <- as.list(as.character(argsDF$V2))
72 names(args) <- argsDF$V1 69 names(args) <- argsDF$V1
73 70
86 83
87 is.letter <- function(x) grepl("[[:alpha:]]", x) 84 is.letter <- function(x) grepl("[[:alpha:]]", x)
88 85
89 #### hsa00010 -> 00010 86 #### hsa00010 -> 00010
90 remove_kegg_prefix <- function(x){ 87 remove_kegg_prefix <- function(x){
88 x = gsub(":","",x)
89 if (substr(x,1,4) == 'path'){
90 x=substr(x,5,nchar(x))
91 }
91 if (is.letter(substr(x,1,3))){ 92 if (is.letter(substr(x,1,3))){
92 x <- substr(x,4,nchar(x)) 93 x <- substr(x,4,nchar(x))
93 } 94 }
94 return(x) 95 return(x)
95 } 96 }
119 120
120 121
121 #read input file or list 122 #read input file or list
122 if (!is.null(args$input)){ 123 if (!is.null(args$input)){
123 tab <- read_file(args$input,header) 124 tab <- read_file(args$input,header)
124 tab <- tab[!apply(is.na(tab) | tab == "", 1, all),] #delete empty rows 125 tab <- data.frame(tab[which(tab[ncol]!=""),])
125 } else { 126 } else {
126 tab <- data.frame(id_list) 127 tab <- data.frame(id_list)
127 ncol=1 128 ncol=1
128 } 129 }
129 130