If I started with some thing like this how will I join it to my code to work or make sense.

# Open a .txt file

 open(seq1, "<seq1.txt") or die $!;

 #Assign open files to arrays

 my @seq1 = <seq1>;
 print "@seq1";
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Didn't try your code, but the syntax for open is usually this:


open(my $fh, "<", "input.txt") 
    or die "cannot open < input.txt: $!";
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Here's how to read records (lines) from a plain text file in the ASCII character encoding:

use strict;
use warnings;

use autodie qw( open close );
use English qw( -no_match_vars );

@ARGV == 1 or die "Usage: perl $PROGRAM_NAME <input file>\n";

my $input_file = shift;

open my $fh, '<:encoding(ASCII)', $input_file;

RECORD:
while (my $record = <$fh>) {
    # Do something with record...
}

close $fh;
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