Entirely uncessarily complex script to colour DNA sequences at arbitrary positions.. because...reasons? Even the help is colourful!

seqcol.sh

#!/bin/bash

# Set colours:
df=$(tput sgr0)
tr=$(tput setaf 1)
tg=$(tput setaf 2)
ty=$(tput setaf 3)
tb=$(tput setaf 4)

usage(){
cat << EOF >&2
Arbitrary colouring of ATGC sequences by providing indexed colour vectors in (pretty much)
pure bash. Colours are fixed for the moment, but can easily be extended or altered by
changing/adding more of the numbers passed to tput in the first couple of lines of the
scripts source code (you'd also want to rename the arguments too etc, probably).

Usage:

$ bash seqcol.sh -r "1,2,3" -g "4,5,6" -y "7,8,9" -b "10,11,12" -s ATGCATCGATCGGCTAGCTA
Yeilds:
${tr}A${df}${tr}T${df}${tr}G${df}${tg}C${df}${tg}A${df}${tg}T${df}${ty}C${df}${ty}G${df}${ty}A${df}${tb}T${df}${tb}C${df}${tb}G${df}GCTAGCTA

Some more advanced usages:

$ bash seqcol.sh -r "\$(seq -s, 1 10)" -y "\$(seq -s, 11 20)" -s ATGCATCGATCGGCTAGCTA
Yields:
${tr}ATGCATCGAT${ty}CGGCTAGCTA${df}

$ bash seqcol.sh -r "\$(seq -s, 1 2 20)" -y "\$(seq -s, 2 2 21)" -s ATGCATCGATCGGCTAGCTA
Yeilds:
${tr}A${ty}T${tr}G${ty}C${tr}A${ty}T${tr}C${ty}G${tr}A${ty}T${tr}C${ty}G${tr}G${ty}C${tr}T${ty}A${tr}G${ty}C${tr}T${ty}A${df}

A thoroughly unecessary use of my time, inspired by this question: https://www.biostars.org/p/342247
EOF
}

for arg in "$@"; do
  shift
  case "$arg" in
        "--help")      set -- "$@" "-h"   ;;
        "--sequence")  set -- "$@" "-s"   ;;
        "--red")       set -- "$@" "-r"   ;;
        "--green")     set -- "$@" "-g"   ;;
        "--yellow")    set -- "$@" "-y"   ;;
        "--blue")      set -- "$@" "-b"   ;;
        *)             set -- "$@" "$arg" ;;
  esac
done
while getopts "hr:g:y:b:s:" OPTION ; do
  case $OPTION in
       s) sequence=$OPTARG ;;
       r) red=$OPTARG      ;;
       g) green=$OPTARG    ;;
       y) yellow=$OPTARG   ;;
       b) blue=$OPTARG     ;;
       h) usage ; exit 0   ;;
  esac
done

in_array() {
# Check if element ($2) is in array ($1)
 ARRAY=$2
 for e in ${ARRAY[*]} ; do
  if [[ "$e" == "$1" ]] ; then
   return 0
  fi
  done
 return 1
}

red(){
printf "${tr}$1${df}"
}
green(){
printf "${tg}$1${df}"
}
yellow(){
printf "${ty}$1${df}"
}
blue(){
printf "${tb}$1${df}"
}

string=$(echo "$sequence" | tr '[:lower:]' '[:upper:]')
IFS=',' read -r -a Rarray <<< "$red"
IFS=',' read -r -a Garray <<< "$green"
IFS=',' read -r -a Yarray <<< "$yellow"
IFS=',' read -r -a Barray <<< "$blue"


for i in $(seq 1 "${#string}") ; do
  if in_array "$i" "${Rarray[*]}" ; then
   red "${string:i-1:1}"
  elif in_array "$i" "${Garray[*]}" ; then
   green "${string:i-1:1}"
  elif in_array "$i" "${Yarray[*]}" ; then
   yellow "${string:i-1:1}"
  elif in_array "$i" "${Barray[*]}" ; then
   blue "${string:i-1:1}"
  else
   printf "${string:i-1:1}"
  fi
done
printf "\n"