Hello! I'm trying to format a code in which I'm trying to create a reverse decoy sequence. So far this is what I've come up with: 

#! usr/bin/perl -w
use strict; 

open (INPUT, "proteins.txt") or die "Couldn't open proteins.txt for re
+ading: $! \n"; 
open (OUTPUT, ">reverse_decoy.txt") or die "Couldn't open reverse_deco
+y.txt for writing: $! \n";

my @protein = <INPUT>; 
print OUTPUT "@protein \n"; 

foreach my $protein (@protein) {
    if ($protein =~ s/^>(.*\n)/> REVERSE DECOY $1/g) { 
    my $header = $protein; 
    print OUTPUT "$header"; 
    }
    else { 
        my $sequence = $protein; 
        $sequence =~ s/\n//; 
        my @reversed_sequence = split(/\s+/, reverse($sequence));
        print OUTPUT "@reversed_sequence\n"; 
        }}

close INPUT; 
close OUTPUT;

[download]

My main difficulty is that even if it reverses the sequence, it only reverses each line, instead of reversing the entire file. For example: >Sequence 1 ABCDEFG HIJKLMN OUTPUT: >Reverse Decoy Sequence 1 GFEDCBA NMLKJIH Goal: >Reverse Decoy Sequence 1 NMLKJIH GFEDCBA If there's any way to switch my order of lines, I think that would help a lot! This way the lines will already be reversed, and then the order of them will be too.

In reply to Switching the Order of Lines by BeckyLynn

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