Struggling to write an R script that searches BLAST with given DNA sequences – General

I’m trying to write an RStudio script that takes an excel file with a list of DNA sequences and searches BLASTn from NCBI with them, obtains the top hit for percent identity and accession number, and exports the results as a csv. The problem I am having is that the results are only showing NA for each DNA sequence in the new csv file instead of providing the expected results. I’ve attached the file that BLAST has been giving me with the NA values. Here is my code:

excel_file <- “C:/Users/rbh6/Documents/BLAST TEST START/TEST_BLAST_RSTUDIO.xlsx”
dna_sequences <- readxl::read_excel(excel_file, sheet = “Sheet1”, col_names = TRUE)

print(head(dna_sequences))

excel_file <- “C:/Users/rbh6/Documents/BLAST TEST START/TEST_BLAST_RSTUDIO.xlsx”
dna_sequences <- readxl::read_excel(excel_file, sheet = “Sheet1”, col_names = TRUE)

print(head(dna_sequences))

blast_results <- lapply(dna_sequences$DNA Sequence, function(sequence) {
result <- tryCatch({
perform_blast(sequence)
}, error = function(e) {
cat(“Error in BLAST search for sequence:”, sequence, “\n”)
cat(“Error message:”, conditionMessage(e), “\n”)
return(rep(NA, 3)) # Return NAs for columns if no match is found
})

if (length(result) == 0) {
return(rep(NA, 3))
} else {
return(result)
}
})

max_length <- max(sapply(blast_results, function(x) max(lengths(x))))

result_df <- data.frame(
Sequence = rep(dna_sequences$DNA Sequence, each = max_length),
Top_Hit_Accession_Number = unlist(lapply(blast_results, function(x) c(x[[1]], rep(NA, max_length – length(x[[1]]))))),
Query_Coverage = unlist(lapply(blast_results, function(x) c(x[[2]], rep(NA, max_length – length(x[[2]]))))),
Percent_Identity = unlist(lapply(blast_results, function(x) c(x[[3]], rep(NA, max_length – length(x[[3]])))))
)

setwd(“C:/Users/rbh6/Documents/BLAST TEST COMPLETED”)
data_Path <- “C:/Users/rbh6/Documents/BLAST TEST COMPLETED”
path <- file.path(data_Path, paste(Sys.Date(), “_BLAST_RESULTS.csv”, sep = “”))
write.csv(result_df, file = path)

cat(“BLAST search and CSV export completed. Results saved in”, path, “\n”)

cat(“BLAST search completed. Displaying results:\n”)
print(blast_results)