perl script to generate six frame sequences

[pony2001mx]

Hi everyone
I wrote a script to generate siz frame sequences (+1 +2 +3 -1 -2 -3 frames). However, it only works on frames +1 +2 +3 -1. For example the following is -3 frame sequence generation. Where is wrong? Note after the script i make an output example. Thank you very much!

#!/bin/perl
use strict;
use warnings;

my $frame = -3;  #when changing to -1 output sequences are ok; but -2 or -3 does not work;
open IN, $ARGV[0];

while (<IN>){
	chomp;
	my $m = length ($_);
	
	if(/^>(\w+)/){
	 print ">$1"."_"."frame"."$frame"."\n";
	 }else{
		my $comprevseq = reverse $_;
		$comprevseq =~ tr/[A,T,C,G]/[T,A,G,C]/; 
		my $frameseq = substr ($comprevseq, abs($frame)-1, $m-abs($frame)+1);
		
		print "$frameseq\n";
	}
}
close IN;

INPUT file

>seq1
ATGC
>seq2
ATGC
>seq3
TTTT

OUTPUT result

>seq1_frame-3
CAT
>seq2_frame-3
CAT
>seq3_frame-3
AA

[SNPsaurus]

This gives the correct answer (and is pretty much your code without the reading in the lines):

#!/bin/perl

my $frame = -3;
$s = "ATGC";

my $m = length ($s);


my $comprevseq = reverse $s;
$comprevseq =~ tr/[A,T,C,G]/[T,A,G,C]/;
my $frameseq = substr ($comprevseq, abs($frame)-1, $m-abs($frame)+1);

print "$frameseq\n";

exit(0);

output:

AT

The fact that the last input in your example works points to the problem being the linefeeds. You do chomp the input. But if the input has windows-type carriage returns and linefeeds there will be an extra invisible character. You can:
local $/ = "\r\n";

so that chomp removes both characters.

[pony2001mx]

Thank you very much, SNPsaurus. You comment is really helpful!