Programming

I am trying to run the following script which is a file format converter. The frame variable in the input file has a file of 3,2,1 which needs to be 0,1,2 respectively i.e. 3 =0 etc.
I have included the tr/// function into the script to do this, however it does not seem to be working
input its
orf00002 111 974 +3 2.94
and output should be
orf00002 Glimmer3 CDS 111 974 2 + 0 note "Glimmer3 prediction" ; colour 3

However, the output is actually

orf00002 Glimmer3 CDS 111 974 2 + 18446744073709551614 note "Glimmer3 prediction" ; colour 3

I would appreciate any help as i just can't see the problem. The script does exactly what it is supposed to do without the tr/// function but with the wrong values for the frame variable

thanks in advance and the script is included below

Brian

Code:

#!/usr/bin/perl -w

while (<>) {
    /(\S+)\s+(\d+)\s+(\d+)\s+([\/+\-])(\d)\s+(\d+)/;    
    $header = $1;
    $start = $2;
    $stop = $3;
    $strand = $4;
    $frame = $5;
    $frame = ~ tr/321/012/; 
    $score = $6;
    if ($strand eq "+"){
        print "$header\tGlimmer3\tCDS\t$start\t$stop\t$score\t$strand\t$frame\tnote \"Glimmer3 prediction\" ; colour 3\n";
    }elsif ($strand eq "-"){
        print "$header\tGlimmer3\tCDS\t$stop\t$start\t$score\t$strand\t$frame\tnote \"Glimmer3 prediction\" ; colour 3\n";
    }
}

Your problem is this line:

Code:

$frame = ~ tr/321/012/;

It will take the number of transformations done by tr (0), invert it bitwise, and assign it to $frame. What you want is:

Code:

$frame =~ tr/321/012/;

Remember, when hunting bugs, these four lines can save you a lot of time:

Code:

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

thanks