convert RNA to amino acid

codon.sh

#!/bin/bash -
#
# SCRIPT: codon
# AUTHOR: Luciano D. Cecere
# DATE: 10/30/2014-06:09:05 PM

PROGRAM=${0##*/}

codon()
{
    local amino slc str=$1

    case $1 in
      auu|auc|aua)		amino=Isoleucine slc=I ;;
      cuu|cuc|cua|cug|uua|uug)	amino=Leucine slc=L ;;
      guu|guc|gua|gug)		amino=Valine slc=V ;;
      uuu|uuc)			amino=Phenylalanine slc=F ;;
      aug)			amino=Methionine slc=M ;;
      ugu|ugc)			amino=Cysteine slc=C ;;
      gcu|gcc|gca|gcg)		amino=Alanine slc=A ;;
      ggu|ggc|gga|ggg)		amino=Glycine slc=G ;;
      ccu|ccc|cca|ccg)		amino=Proline slc=P ;;
      acu|acc|aca|acg)		amino=Threonine slc=U ;;
      ucu|ucc|uca|ucg|agu|agc)	amino=Serine slc=S ;;
      uau|uac)			amino=Throsine slc=Y ;;
      ugg)			amino=Tryptophan slc=W ;;
      caa|cag)			amino=Glutamine slc=Q ;;
      aau|aac)			amino=Asparagine slc=N ;;
      cau|cac)			amino=Histidine slc=H ;;
      gaa|gag)			amino="Glutamic Acid" slc=E ;;
      gau|gac)			amino="Aspartic Acid" slc=D ;;
      aaa|aag)			amino=Lysine slc=K ;;
      cgu|cgc|cga|cgg|aga|agg)	amino=Arginine slc=F ;;
      uaa|uag|uga)		amino="Stop amino" slc=STOP ;;
      *)			amino="Invalid codon" slc=? ;;
    esac

	declare -u $str
	cat <<-eof
	RNA Codon:	$( tr a-z A-Z <<< $str)
	Amino Acid:	$amino
	SLC:		$slc
	eof
}

chart()
{
	cat <<-eof
	   AMINO ACID  SLC	   RNA CODONS
	 =====================================================
	 ISOLEUCINE	I	AUU, AUC, AUA
	 LEUCINE	L	CUU, CUC, CUA, CUG, UUA, UUG
	 VALINE		V	GUU, GUC, GUA, GUG
	 PHENYLALANINE	F	UUU, UUC
	 METHIONINE	M	AUG
	 CYSTEINE	C	UGU, UGC
	 ALANINE	A	GCU, GCC, GCA, GCG
	 GLYCINE	G	GGU, GGC, GGA, GGG
	 PROLINE	P	CCU, CCC, CCA, CCG
	 THREONINE	U	ACU, ACC, ACA, ACG
	 SERINE		S	UCU, UCC, UCA, UCG, AGU, AGC
	 THROSINE	Y	UAU, UAC
	 TRYPTOPHAN	W	UGG
	 GLUTAMINE	Q	CAA, CAG
	 ASPARAGINE	N	AAU, AAC
	 HISTIDINE	H	CAU, CAC
	 GLUTAMIC ACID	E	GAA, GAG
	 ASPARTIC ACID	D	GAU, GAC
	 LYSINE		K	AAA, AAG
	 ARGININE	F	CGU, CGC, CGA, CGG, AGA, AGG
	 STOP CODONS   STOP	UAA, UAG, UGA
	 =====================================================
	eof
}

help()
{
	cat <<-eof
	$PROGRAM - convert RNA codon to Amino Acid
	usage: $PROGRAM [-option] [aucg]
	Options:	-c --chart	View codon chart
	                -h --help	Display this help
	eof
}

if [ $# -eq 0 ]; then
  help
  echo
  chart
  exit 1
fi

declare -l codon=$1

case $codon in
  -c|--chart)	chart
		;;
  -h|--help)	help
		;;
  *)		codon "${codon:0:3}"
esac