Hi everyone,

I try to run one script, and I get this message, I do not know what it's means

Use of uninitialized value $out in concatenation (.) or string at blas
+tall_modificado line 20.
readline() on closed filehandle $IN at blastall_modificado line 26.
Use of uninitialized value $out in concatenation (.) or string at blas
+tall_modificado line 80.
 is done
[download]

line

20       open my $OUT, '>', "$out.out";

26       while  (my $line = <$IN>){

79       print "$out is done\n";
[download]

Now the errors are :

Global symbol "$out" requires explicit package name at script line 20.

Global symbol "$out" requires explicit package name at script line 79.

Execution of script aborted due to compilation errors.

#!/usr/bin/perl 


use warnings;
use strict;

my @outs;
my %grupos1;
my %grupos2;
my @split; 
#my $out;    
my @element2; 
my @element1; 


open my $IN , '<', " $ARGV[0]"; 
open my $OUT, '>', "$out.out" or die "open failed: $!\n";



#########################----

while  (my $line = <$IN>){
    chomp $line;
    my @split = split /\t/, $line;
    my $id1 = join ("\t", @split);

    if (!defined $grupos1{$id1}) {
        $grupos1{$id1}= [];
    } #close defined hash %grupos1 if

    push @{$grupos1{$id1}}, [$split[0],$split[1],$split[2],$split[3],$
+split[4]];  

}# close while
close $IN;


#-----------------------------------
open my $IN2 , '<', "$ARGV[1]"; 

while (my $line2=<$IN2>) {
    chomp $line2;                  
    my @split2 = split /\t/, $line2;
    my $id2 = join ("\t", @split); 

    if (!defined $grupos2{$id2}) {
            $grupos2{$id2}= [];

    } #close defined hash %grupos2 if

    push @{$grupos2{$id2}}, [$split2[12],$split2[1], $split2[10], $spl
+it2[11]];  

} #close while

close $IN2;


foreach my $key1 ( sort keys %grupos1 ) {
    for my $element1 ( @{ $grupos1{$key1} } ) {    #derefrence

        foreach my $key2 ( sort keys %grupos2 ) {
            for my $element2 ( @{ $grupos2{$key2} } ) {

                if ( $element1->[0] eq $element2->[0]){

                    my $new_start= $element1->[2]+$element2->[2]; 
                    my $new_end= $element1->[3]+$element2->[3];  
                    
                    print  $OUT, "$element1->[1]\t$new_start\t$new_end
+\t$element2[1]\t.\t$element1[4].\t.$element2[0]\n";
                    
                } ## end if
            }    #end foreach key1
        }
    }    #end foreach key2
} #end foreach key1
print "$out is done\n";
%grupos1 = (); #empty hash
%grupos2 = (); #empty hash
close $OUT;
#} #close genome
[download]

Thanks you so much for your help

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.