$line is a scalar variable that you declare in line 9. $line[$i] is an element of an array named @line, which is a totally different (undeclared) variable that has no relationship to the scalar named $line.

The scalar variable $i makes its first appearance in your script in line 11. What value is it supposed to contain? If you don't declare it, and don't assign it a value, it's probably not going to do what you need it to do.

You're missing a semicolon after the substr(...) call on line 14. (It's usually a good idea to look at the line right above where syntax errors are reported.)

Finally: Install perltidy and pass your script through it. Judicious use of white-space makes code more readable, and errors easier to detect.

These only address the superficial issues: the error messages you're seeing. Once you fix those issues, it becomes time to debug the logic.

open (my $fhConditions, "<a.txt"); 
my $l=6;
open (my $read, "<b.txt");
my @e = <$read>;
my $d = join('', @e );
$d =~ s/\s+//g;
while (<$fhConditions>) {
    push (my @line, $_);
$count++;
}
for ($i = 0; $i < $count; $i++)
{
my @pos = my $line[$i] =~ /chr*\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/;
}
}
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this the code modified after the suggestions. but still i am getting some error

yntax error at restriction.pl line 13, near "$line["
Execution of restriction.pl aborted due to compilation errors.
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You should remove my from line 13. It doesn't belong there and is causing this error.

Hi!

To get rid of the errors, read the error-messages.

• line 11: you use $line[$i], but you have defined $line as a scalar (not an array)
• line 11: you use $i, but have never defined it ... (hint: and you don't need it)
• line 15: a syntax error is often caused by a missing semicolon the line before
• line 15: often error-messages are created due to errors before ... so solve the first three errors and check if this one prevails

In addition to the points made above by davido and Ratazong, the line:

if($pos[0] =/[0-9]/)
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should be written as:

if ($pos[0] =~ /[0-9]/)
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Likewise for the line:

if($pos[1] =/[0-9]/)
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HTH,

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

i am not getting errors as well as output

That’s because you’ve removed

use strict;
use warnings;
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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.
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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;
    ...
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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