#!/usr/bin/perl  -w

#  This script will ask for the name of a file
#  containing DNA sequence and validate each
#  line of sequence.  If invalid bases are found,
#  the offending line number(s) are reported.
#  Author:  MyName
#    Version 1.2   21 Feb 04   added line number output
#    Version 1.1   24 Dec 03   output invalid base
#    Version 1.0   15 Sep 03   initial version

use strict;
my ($filename, $line, $lnum);

#   Notice that when we print a question we do
#   not include a newline since we want the user's
#   typed response to be entered on the same line
print   "Enter DNA sequence file name:  ";
$filename  =  <STDIN>;

#  Open the file, or die with an error message
open(SEQFIL, "$filename") or
    die "Cannot open file $filename\n";

# Count line numbers for error reporting
$lnum = 0;
while ( $line = <SEQFIL> ) {
  $lnum++;;
  chomp($line);
  if ( $line  =~  /([^ACGTacgt])/ ) {
    print "Invalid DNA sequence ($1) on line $lnum\n";
  }
}  # end of while <SEQFIL>
close SEQFIL;