Suggestion for Alternative Solution Due to KEGG API Instability

[KitHubb]

Hello, Chen YANG!

This is KitHubb, and I'm still using ggpicrust2 with great success. Congratulations on its registration on CRAN!

I've encountered frequent instability with the KEGG server while using it, and I’d like to suggest an additional database for annotating KEGG pathway information in Ko.

Here are the details for the proposed datasource and the R code for processing:

• Datasource: Download htext
• R Code:

library(readr)
library(stringr)
[KO_20240812_ff.csv](https://github.com/user-attachments/files/16577153/KO_20240812_ff.csv)


# Read and process KO data
liness <- read.delim2("./KO")
lines <- liness$X.D

# Initialize variables
level_A <- level_B <- level_C <- NA
data <- list()

# Process hierarchy
for (line in lines) {
  line <- trimws(line)
  
  if (startsWith(line, "A")) {
    content <- trimws(substr(line, 2, nchar(line))) 
    level_A <- substring(content, 2)
  } else if (startsWith(line, "B")) {
    content <- trimws(substr(line, 2, nchar(line))) 
    level_B <- substring(content, 2)
  } else if (startsWith(line, "C")) {
    content <- trimws(substr(line, 2, nchar(line))) 
    level_C <- substring(content, 2)
  } else if (startsWith(line, "D")) {
    content <- trimws(substr(line, 2, nchar(line))) 
    level_D <- substring(content, 2)
    data <- append(data, list(c(level_A, level_B, level_C, level_D)))
  }
}

# Convert to data frame
data <- do.call(rbind, data)
colnames(data) <- c("Level1", "Level2", "Level3", "KO")
data2 <- as.data.frame(data, stringsAsFactors = FALSE)

# Flattened data frame
print(data2)
dim(data2) #  61655     4

# Extract EC, Ko, Kegg access number
data3 <- data2
data3$KEGG <- paste0("ko", sub(".*(\\d{5})\\]$", "\\1", data3$Level3))
data3$EC <- paste0("EC:", str_extract(data3$KO, "(?<=EC:)[^]]+"))
data3$KO_num <- paste0("K", substr(x = data3$KO , start = 1, stop = 6))
data3[is.na(data3)] <- ""

library(data.table)
fwrite(data3, "./KO_20240812_ff.csv")

I hope you find this suggestion helpful.
Let me know if you have any questions or need further information.

Best regards,
KitHubb