Bash script to screen the primer of interest in your file, including it's reverse sequence, its compliment, and it's reverse compliment.

primer_screen.sh

#!/bin/bash

#HOW TO USE: sh primer_screen.sh <primer> <path to file with sequences>

#Simple bash script to quickly screen the primer of interest in your file. 
#The script will screen for your primer, it's reverse sequence, its compliment, and it's reverse compliment. 
#If a perimer is found, the terminal will print text in red with the primer sequence and the
#number of times the primer is present in the file. 

primer1=$1
fastq=$2
RED='\033[0;31m'
NC='\033[0m' # No Color

primer2=$(echo "$1" | rev)
primer3=$(echo "$1" | rev | tr ATGCatgcNn TACGtacgNn)
primer4=$(echo "$1" | tr ATGCatgcNn TACGtacgNn)

for primer in $primer1 $primer2 $primer3 $primer4
do
        num=$(grep -c "${primer}" ${fastq})

        if [ $num -ne "0" ]; then
                printf "${RED}The primer ${primer} is found in ${num} sequences in the file ${fastq}\n${NC}"
        else
                printf "The primer ${primer} is found in ${num} sequences in the file ${fastq}\n"
        fi
done
printf "\n"