Mercurial > repos > proteore > proteore_prot_features

comparison protein_features.R @ 5:867d47ff782c draft

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planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty
author proteore
date Wed, 14 Mar 2018 12:04:32 -0400
parents bfc679370c64
children fc0118aa432a
comparison
equal deleted inserted replaced
4:bbb17bca9ec1 5:867d47ff782c
68 input = c() 68 input = c()
69 for (row in as.character(file[,ncol])) { 69 for (row in as.character(file[,ncol])) {
70 input = c(input, strsplit(row, ";")[[1]][1]) 70 input = c(input, strsplit(row, ";")[[1]][1])
71 } 71 }
72 } 72 }
73
74 # Read reference file
73 nextprot_file = args$nextprot 75 nextprot_file = args$nextprot
74 nextprot = human_id_map = read.table(nextprot_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "") 76 nextprot = read.table(nextprot_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "", quote = "")
77
78 # Parse arguments
75 typeid = args$type 79 typeid = args$type
76 P1_args = strsplit(args$argsP1, ",")[[1]] 80 P1_args = strsplit(args$argsP1, ",")[[1]]
77 P2_args = strsplit(args$argsP2, ",")[[1]] 81 P2_args = strsplit(args$argsP2, ",")[[1]]
78 P3_args = strsplit(args$argsP3, ",")[[1]] 82 P3_args = strsplit(args$argsP3, ",")[[1]]
79 output = args$output 83 output = args$output