Creating a condition on a bash script

Shell Programming and Scripting
1

I wrote a code to find codons in a DNA string. The only problem I have is how do I make the code only work for a file with DNA. This means the file only has the characters a,c,g,t and no white space characters.

2

How about:

if ! grep -q '[^acgt]' file
then
  ...
fi

or

if grep -q '[^acgt]' file
then
  echo "This file contains non-acgt characters"
  exit 1
fi
3

What Scrutinizer suggested will work if your "file with DNA" is a UNIX formatted text file that contains zero or more lines where each line contains a DNA string of zero or more characters.

If the files contain a single DNA string with no terminating <newline> character (which is what is specified in post #1), you'll need something more like:

#!/bin/bash
IAm=${0##*/}
tmpfile="$IAm.$$"
trap 'rm -f "$tmpfile"' 0
if ! tr -d 'acgt' < "$1" > "$tmpfile" || [ -s "$tmpfile" ]
then	printf 'File "%s" is not a DNA file.  Exiting.\n' "$1" >&2
	exit 1
fi
printf 'File "%s" is a DNA file.  Continuing...\n' "$1"
# Do whatever you want to do with the specified DNA file...

This script requires one operand that is a pathname of the file you want to test.

4

Fair enough. Just out of curiosity: wouldn't something like:

(cat /file/in/question - < printf '\n') | ...

suffice? This would either add an empty line (which would be irrelevant) or terminate the last line properly. No?

bakunin