Re: =~ matches non-existent symbols

[graff]

Here's how I would modify the OP script:

#!/usr/bin/perl

use strict;
use warnings;

$/ = undef;     # slurp-mode for input, just in case
while ( <> ) {  # reads stdin or all file names in ARGV
    s/\s+//g;   # remove whitespace
    tr/ACGTacgt//d; # remove all acgt

    if ( length() ) { # anything left?
        print "$ARGV bad content: $_\n";
    } else {
        print "$ARGV all clean!\n";
    }
}

Using  while (<>) is good (even with slurp-mode input) because that way you can pipe data from any other process as input to the script, or you can put one or more file names on the command line (e.g. "*.txt").

When you read multiple input files in one run, putting "$ARGV" in the print statements tells you which files are good or bad.

[Anonymous Monk]

Thanks, graff! But what if I need to do further manipulations with the data from the file later in the same program?

[graff]

what if I need to do further manipulations with the data from the file later in the same program?

Presumably, the manipulation will depend on whether the file content is "good" or "bad" - in either case, just save a copy of $_ to some other variable after white-space removal but before removing "acgt"; then pass that copy to whatever function you write to do the manipulation (either good or bad).

[Laurent_R]

This will be for a second step. Right now, you are saying that your file contains only /ACGT/i but that your validation procedure fails. Many of us think that it is likely that your file contains at least one line feed or carriage return character or a combination of both. The important thing right now is to find out what are the hidden characters that lead your validation subroutine to fail. Once you know that, you can modify your original program or your regex to take the findings into account.

[ikegami]

That considers acegt a valid input.

[graff]

I saved my script as posted to "/tmp/j.pl", and ran it as follows:

echo acegt | /tmp/j.pl

The output was:

- bad content: e

Did you find some other way to run it that yields different results?

[ikegami]

Me bad. Comment deleted.