DNA_2_BINARY.sh

#!/bin/bash
#small code to make binary from the DNA fasta sequence
echo "
    DNA_2_BINARY.sh - written by Abhijeet Singh (abhijeetsingh.aau@gmail.com)

    Translating DNA bases to 0 and 1

"

if [ "$#" -gt 0 ]; then
	filename=$1
else
	echo "please provide the name of your fasta file"
	read filename
fi
fasta_file=filename
cut -d ' ' -f1 "${!fasta_file}" > "${!fasta_file}"_trimhead
awk 'BEGIN{RS=">"}NR>1{sub("\n","\t"); gsub("\n",""); print RS$0}' "${!fasta_file}"_trimhead > "${!fasta_file}"_tab
awk '{print $1}' < "${!fasta_file}"_tab > "${!fasta_file}"_tab_col1
awk '{print $2}' < "${!fasta_file}"_tab > "${!fasta_file}"_tab_col2
echo "
-----------------------------------
The codes used for translation are:
    A=00
        T=11
            C=01
                G=10
-----------------------------------"
sed 's/A/00/g;s/T/11/g;s/C/01/g;s/G/10/g' "${!fasta_file}"_tab_col2 > "${!fasta_file}"_tab_col2_2
paste "${!fasta_file}"_tab_col1 "${!fasta_file}"_tab_col2_2 | column -s $'\n' -t > "${!fasta_file}"_binary.tmp.txt
sed 's/\t/\n/g' < "${!fasta_file}"_binary.tmp.txt > "${!fasta_file}"_binary.txt
rm -f "${!fasta_file}"{_trimhead,_tab,_tab_col1,_tab_col2,_tab_col2_2,_binary.tmp.txt}
echo "                            ========================="
echo "your result file is ---->>> ${!fasta_file}_binary.txt"
echo "                            ========================="