How to determine n and c terminal nucleotide bases from fasta sequences via R or bash scripting?

Question

[prithvi.mastermind]

I want to determine n and c terminal nucleotide bases from fasta sequences via R or bash scripting. Can anybody please suggest some corrections in my prepared R code as it is assigning a fixed length of nucleotide bases which is not the actual case. Please help to modify the current code or suggest some bash commands.

This is my input file:

>MN200573.1_India
AACCCAAAAAATCCACGTGAAAATAAGCTGAAACAACCAGGAGACAGAGCAGATGGACAGCCAGCAGGAG
ACAGAGCAGATGGACAGCCAGCAGGTGATAGAGCAGCTGGACAACCAGCAGGTGATAGAGCAGATGGACA
GCCAGCAGGCGATAGAGCAGCTGGACAGCCAGCAGGCGATAGAGCAGATGGACAGCCAGCAGGAGATAGA
GCAGCTGGACAGCCAGCAGGCGATAGAGCAGATGGACAGCCAGCAGGAGATAGAGCAGCTGGACAGCCAG
CAGGCGATAGAGCAGATGGACAGCCAGCAGGAGATAGAGCAGCTGGACAACCAGCAGGTGATAGAGCAGC
TGGACAACCAGCAGGAGATAGAGCAGATGGACAACCAGCAGGAGATAGAGCAGCTGGACAGCCAGCAGGA
GATAGAGCAGCTGGACAGCCAGCAGGAGATAGAGCAGCTGGACAGCCAGCAGGAGATAGAGCAGCTGGAC
AGCCAGCAGGAAATGGTGCAGGTGGACAGGCAGCAGGAGGAAATGCGGCAAACAAGAAGGCAGAAGACGC
AGGAGGAAACGCAGGAGGACAGGGACAAAATAATGAAGGTGCGAATGCCCCAAATGAAAAGTCTGTGAAA
GAATACCTAGATAAAGTTAGA

# Load required library

if (!requireNamespace("Biostrings", quietly = TRUE)) {
  install.packages("BiocManager")
  BiocManager::install("Biostrings")
}
library(Biostrings)

# Read the FASTA file
fasta_file <- "India.txt"
sequences <- readDNAStringSet(fasta_file, format = "fasta")

# Initialize a data frame to store the results
results <- data.frame(
  Sequence_Name = names(sequences),
  N_Terminal = character(length(sequences)),
  C_Terminal = character(length(sequences)),
  stringsAsFactors = FALSE
)

# Extract the N-terminal (first 10 residues) and C-terminal (last 10 residues)
for (i in seq_along(sequences)) {
  seq <- as.character(sequences[[i]])
  n_terminal <- substr(seq, 1, 10)
  c_terminal <- substr(seq, nchar(seq) - 9, nchar(seq))

  results[i, "N_Terminal"] <- n_terminal
  results[i, "C_Terminal"] <- c_terminal
}

# Write the results to a CSV file
output_file <- "N_C_Terminals.csv"
write.csv(results, output_file, row.names = FALSE)

cat("N-terminal and C-terminal sequences extracted and saved to", output_file, "\n")

[Mensur Dlakic]

N- and C-terminal are protein terms. Nucleotide sequences have 5' and 3' ends.

Answer 1

[Pierre Lindenbaum]

linearize and extract:

 awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}'  input.fasta  |\
awk -F '\t' '{N=length($2);printf("%s\t%s\t%s\n",$1,substr($2,1,10),substr($2,N-9));}'

Answer 2

[bk11]

In bash, I m not sure though if you wanted to perform something like below:

#!/bin/bash

input_file=$1
n_length=10
c_length=10

while read -r line; do
  if [[ $line == ">"* ]]; then
    echo "$line"
  else
    n_term=$(echo "$line" | cut -c1-$n_length)
    c_term=$(echo "$line" | rev | cut -c1-$c_length | rev)
    echo "N-terminal: $n_term"
    echo "C-terminal: $c_term"
    echo
  fi
done < "$input_file"

./bash.sh india.fasta
>MN200573.1_India
N-terminal: AACCCAAAAA
C-terminal: CCAGCAGGAG

N-terminal: ACAGAGCAGA
C-terminal: CAGATGGACA

N-terminal: GCCAGCAGGC
C-terminal: AGGAGATAGA

N-terminal: GCAGCTGGAC
C-terminal: GGACAGCCAG

N-terminal: CAGGCGATAG
C-terminal: ATAGAGCAGC

N-terminal: TGGACAACCA
C-terminal: GCCAGCAGGA

N-terminal: GATAGAGCAG
C-terminal: GCAGCTGGAC

N-terminal: AGCCAGCAGG
C-terminal: CAGAAGACGC

N-terminal: AGGAGGAAAC
C-terminal: GTCTGTGAAA

N-terminal: GAATACCTAG
C-terminal: TAAAGTTAGA