Re^2: How to get rid of the errors in my perl script

i have made all the possible corrections. but still i fail to get the proper output.

open (my $fhConditions, "<1.txt"); 
my $l=6;
open (my $read, "<2.txt");
my @e = <$read>;
my $d = join('', @e );
$d =~ s/\s+//g;
while (<$fhConditions>) {
    push (my @line, $_);
my $count++;
}
for (my $i = 0; $i <$count; $i++)
{
my @pos = $line[$i] =~ /chr[0-9]\s+(.+?)\s/g;
if($pos[0] =~/[0-9]/)
{
my $match = substr($d,$pos[0],$l);
print "$line[$i]" if $match =~m/AAGCTT/;
}
if($pos[1] =~/[0-9]/)
{
my $a = $pos[0]-$l;
my $match = substr($d,$a,$l);
print "$line[$i]" if $match =~m/AAGCTT/;
}
}
[download]

i doubt first of all its not getting the values it self from the array. i am not getting errors as well as output

Comment on Re^2: How to get rid of the errors in my perl script Download Code

Replies are listed 'Best First'.
Re^3: How to get rid of the errors in my perl script by Athanasius (Archbishop) on Aug 09, 2012 at 14:57 UTC
i am not getting errors as well as output That’s because you’ve removed `use strict; use warnings;` [download] from the head of your script, although they were there in the original. With `use strict` restored, the errors return: `Global symbol "$count" requires explicit package name at test.pl line +13. Global symbol "@line" requires explicit package name at test.pl line 1 +5. Global symbol "@line" requires explicit package name at test.pl line 1 +9. Global symbol "@line" requires explicit package name at test.pl line 2 +5. test.pl had compilation errors.` [download] You need to declare `my $count` and `my @line` before the `while` loop, so that they will still be visible in the following `for` loop: `... my (@line, $count); while (<$fhConditions>) { push @line, $_; $count++; } for (my $i = 0; $i < $count; $i++) { my @pos = $line[$i] =~ /chr[0-9]\s+(.+?)\s/g; ...` [download] See the section “Scope” in the “Functions” chapter of chromatic’s Modern Perl, available free online at http://modernperlbooks.com/books/modern_perl/. Note: In your original question, you gave a sample of the contents of your first input file (`1.txt`), but not of the second (`2.txt`), so it’s difficult to see what your script is trying to do. Athanasius <°(((>< contra mundum	[reply] [d/l] [select]

Replies are listed 'Best First'.

Re^3: How to get rid of the errors in my perl script
by Athanasius (Archbishop) on Aug 09, 2012 at 14:57 UTC

i am not getting errors as well as output

That’s because you’ve removed

use strict;
use warnings;
[download]

from the head of your script, although they were there in the original. With use strict restored, the errors return:

Global symbol "$count" requires explicit package name at test.pl line 
+13.
Global symbol "@line" requires explicit package name at test.pl line 1
+5.
Global symbol "@line" requires explicit package name at test.pl line 1
+9.
Global symbol "@line" requires explicit package name at test.pl line 2
+5.
test.pl had compilation errors.
[download]

You need to declare my $count and my @line before the while loop, so that they will still be visible in the following for loop:

...
my (@line, $count);

while (<$fhConditions>)
{
    push @line, $_;
    $count++;
}

for (my $i = 0; $i < $count; $i++)
{
    my @pos = $line[$i] =~ /chr[0-9]\s+(.+?)\s/g;
    ...
[download]

See the section “Scope” in the “Functions” chapter of chromatic’s Modern Perl, available free online at http://modernperlbooks.com/books/modern_perl/.

Note: In your original question, you gave a sample of the contents of your first input file (1.txt), but not of the second (2.txt), so it’s difficult to see what your script is trying to do.

Athanasius <°(((>< contra mundum

[reply]
[d/l]
[select]