|
|
@@ -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
|
|
|
)
|
|
|
|
|
|
###############################################
|
