#!/bin/bash

# Test whether a fasta file is nucleic acid or protein

# Read arguments from the command line, and set variables to
# represent the arguments
infile=$1
outfile=$2

# process the input file

result=`cat $infile | grep -v '^>' | grep -i -e [FPEJLZOIQ*X] |wc -l`
echo $result

if (($result > 0))
then
    msg="$infile contains protein."
else
    msg="$infile contains DNA."
fi


# output the result
echo $msg > $outfile