update annotation format

emapperx.R

@@ -18,9 +18,9 @@ script_dir <- dirname(strsplit(commandArgs(trailingOnly = FALSE)[4],"=")[[1]][2]
 # test input 
 ###############################################
 # argv <- list()
-# argv$emapper_anno <- 'example_data/my.emapper.annotations'
-# argv$proteins <- 'example_data/Sind.pep.fasta'
-# script_dir <- '/home/zhxd/workspace/Genomics/43.ProteinFunctionAnnotation/emcp'
+# argv$emapper_anno <- 'out.emapper.annotations'
+# argv$proteins <- 'proteins.fa'
+# script_dir <- 'emcp'
 
 library(tidyverse, quietly = TRUE)
 library(formattable, quietly = TRUE)
@@ -36,12 +36,12 @@ emapper <- read_delim(argv$emapper_anno,
                       "\t", escape_double = FALSE, col_names = FALSE, 
                       comment = "#", trim_ws = TRUE) %>%
   dplyr::select(GID = X1, 
-                COG = X10,
-                Gene_Name = X11,
-                Gene_Symbol = X12,
-                GO = X13,
-                KO = X15,
-                Pathway = X16
+                COG = X7,
+                Gene_Name = X8,
+                Gene_Symbol = X9,
+                GO = X11,
+                KO = X12,
+                Pathway = X13
                 )
 
 ###############################################